Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	TCF7L2
Previous Symbol	TCF4
Symbol Alias	TCF-4
Approved Name	transcription factor 7-like 2 (T-cell specific, HMG-box)
Location	10q25.3
Position	chr10:112950250-113167678, 1
External Links	HGNC: 11641 Entrez Gene: 6934 Ensembl: ENSG00000148737 UCSC: uc001lae.4
No. of Studies	1 (Positive: 1; Negative: 0; trend: 0)
Overlap with SZ?	NO
Overlap with MDD?	NO

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Cuellar-Barboza, A. B., 2016	SNP: rs6585194, rs6585195, rs11196175, rs7924080, rs11196201, rs11196203, rs12255372, rs7087006, rs3750804, rs12184389, rs11196224, rs7085532, rs11196229, rs290475, rs6585209, rs1362943, rs7919185, rs290487, rs1885510, rs7917983, rs7895307, rs4132670, rs3750805, rs12772424, rs10787476, rs290484 Haplotype: rs7895307 - rs12772424(G-T)	P(BMI-unadj)-value=0.57; P(BMI-adj)-value=0.56; P(TCF7L2-BMI interaction)-value=0.042. Gene-level results were consistent with the single SNP results, showing no evidence of a marginal effect of TCF7L2, with (p = 0.56) or without (p = 0.57) BMI adjustment, but a significant TCF7L2-BMI interaction effect (p = 0.042).	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 81)

GO terms by PBA (count: 4)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0043565	sequence-specific DNA binding	molecular function	IDA[14661054]; IMP[16532032]	29
GO:0007420	brain development	biological process	IBA	25
GO:0003700	sequence-specific DNA binding transcription factor activity	molecular function	IDA[9727977]	66
GO:0005634	nucleus	cellular component	IDA[16532032]	283

GO terms by database search (count: 77)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0051897	positive regulation of protein kinase B signaling	biological process	IMP[19386626]	11
GO:0021915	neural tube development	biological process	IEA	3
GO:0048641	regulation of skeletal muscle tissue development	biological process	IEA	1
GO:0030538	embryonic genitalia morphogenesis	biological process	IEA	2
GO:0008013	beta-catenin binding	molecular function	IDA[9065401]; IPI[12408825]	14
GO:2000675	negative regulation of type B pancreatic cell apoptotic process	biological process	IDA[18071026]	3
GO:0048619	embryonic hindgut morphogenesis	biological process	IEA	1
GO:0045722	positive regulation of gluconeogenesis	biological process	IEA	1
GO:0045892	negative regulation of transcription, DNA-templated	biological process	IDA[12799378]; IMP[16532032]	43
GO:0035257	nuclear hormone receptor binding	molecular function	IPI[12799378]	5
GO:0031016	pancreas development	biological process	TAS[18216022]	2
GO:0060325	face morphogenesis	biological process	IEA	2
GO:0046621	negative regulation of organ growth	biological process	IEA	3
GO:0043065	positive regulation of apoptotic process	biological process	IEA	25
GO:0048660	regulation of smooth muscle cell proliferation	biological process	IMP[17122440]	2
GO:1901142	insulin metabolic process	biological process	IEA	1
GO:0043588	skin development	biological process	IEA	3
GO:0060070	canonical Wnt signaling pathway	biological process	IC[9065401]	9
GO:0005654	nucleoplasm	cellular component	IDA; TAS	163
GO:0044212	transcription regulatory region DNA binding	molecular function	IDA[20128911]	17
GO:0045295	gamma-catenin binding	molecular function	IPI[14661054]	2
GO:0001568	blood vessel development	biological process	IMP[15578569]	3
GO:0090090	negative regulation of canonical Wnt signaling pathway	biological process	IMP[16532032]	9
GO:0044334	canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition	biological process	IMP[17072303]	1
GO:0035019	somatic stem cell maintenance	biological process	IEA	6
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	biological process	IDA[19168596]	91
GO:2001237	negative regulation of extrinsic apoptotic signaling pathway	biological process	IDA[18071026]	6
GO:0016605	PML body	cellular component	IEA	7
GO:0043433	negative regulation of sequence-specific DNA binding transcription factor activity	biological process	IDA[12799378]	6
GO:0032092	positive regulation of protein binding	biological process	IDA[12799378]	2
GO:0006006	glucose metabolic process	biological process	IEA	10
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	biological process	IDA[12799378]	62
GO:0030282	bone mineralization	biological process	IEA	2
GO:0032252	secretory granule localization	biological process	IEA	2
GO:0010909	positive regulation of heparan sulfate proteoglycan biosynthetic process	biological process	IMP[15853773]	1
GO:0043570	maintenance of DNA repeat elements	biological process	IMP[18755497]	1
GO:0045599	negative regulation of fat cell differentiation	biological process	IEA	7
GO:0048699	generation of neurons	biological process	IBA	3
GO:0032993	protein-DNA complex	cellular component	IDA[14661054]	1
GO:0070016	armadillo repeat domain binding	molecular function	IPI[12408825]	1
GO:0008283	cell proliferation	biological process	IMP[12408868]	37
GO:0031641	regulation of myelination	biological process	IEA	4
GO:0019901	protein kinase binding	molecular function	IPI[16714285]	29
GO:0035264	multicellular organism growth	biological process	IEA	9
GO:0009791	post-embryonic development	biological process	IEA	10
GO:0007050	cell cycle arrest	biological process	IMP[12408868]	10
GO:0048625	myoblast fate commitment	biological process	IDA[10937998]	1
GO:0035411	catenin import into nucleus	biological process	IEA	2
GO:0048713	regulation of oligodendrocyte differentiation	biological process	IEA	2
GO:0003682	chromatin binding	molecular function	IBA	23
GO:0005977	glycogen metabolic process	biological process	IEA	5
GO:0001103	RNA polymerase II repressing transcription factor binding	molecular function	IPI[19443654]	2
GO:0009749	response to glucose	biological process	ISS[19168596]	8
GO:0006351	transcription, DNA-templated	biological process	IEA	103
GO:0005515	protein binding	molecular function	IPI[11713475]	563
GO:0042475	odontogenesis of dentin-containing tooth	biological process	IEA	8
GO:0061178	regulation of insulin secretion involved in cellular response to glucose stimulus	biological process	IEA	5
GO:0000790	nuclear chromatin	cellular component	IDA[19443654]	7
GO:0032350	regulation of hormone metabolic process	biological process	IDA[15525634]	1
GO:0048557	embryonic digestive tract morphogenesis	biological process	IEA	4
GO:0009267	cellular response to starvation	biological process	IEA	6
GO:0014003	oligodendrocyte development	biological process	IEA	2
GO:0042593	glucose homeostasis	biological process	IDA[15525634]	19
GO:0005737	cytoplasm	cellular component	IDA	322
GO:0050679	positive regulation of epithelial cell proliferation	biological process	IEA	9
GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	molecular function	IDA[19443654]	23
GO:0046827	positive regulation of protein export from nucleus	biological process	IMP[19386626]	3
GO:0010867	positive regulation of triglyceride biosynthetic process	biological process	IEA	1
GO:0070369	beta-catenin-TCF7L2 complex	cellular component	IDA[9065401]	1
GO:0005667	transcription factor complex	cellular component	IBA	18
GO:0006357	regulation of transcription from RNA polymerase II promoter	biological process	IDA[9727977]	21
GO:0021983	pituitary gland development	biological process	IEA	4
GO:0030514	negative regulation of BMP signaling pathway	biological process	IEA	1
GO:0045444	fat cell differentiation	biological process	IDA[10937998]	6
GO:0032024	positive regulation of insulin secretion	biological process	IDA[18071026]; IMP[19386626]	7
GO:0040037	negative regulation of fibroblast growth factor receptor signaling pathway	biological process	IEA	1
GO:0008134	transcription factor binding	molecular function	IPI[16007074]	28

Gene related KEGG pathways (count: 9)

KEGG pathways by PBA (count: 2)

ID	Name	No. of Genes in BDgene	Brief Description
hsa05217	Basal cell carcinoma	8
hsa05221	Acute myeloid leukemia	7

KEGG pathways by database search (count: 7)

ID	Name	No. of Genes in BDgene
hsa05210	Colorectal cancer	14
hsa04520	Adherens junction	11
hsa05213	Endometrial cancer	10
hsa05215	Prostate cancer	18
hsa05216	Thyroid cancer	4
hsa04310	Wnt signaling pathway	20
hsa04916	Melanogenesis	16

Gene related BioCarta pathways (count: 0)

Gene related interactors from protein-protein interactions data in HPRD (count: 7)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
TCF7L2	EP300	NO	in vitro;in vivo	12861022
TCF7L2	JUP	NO	in vitro	11711551
TCF7L2	CTNNBIP1	NO	in vitro;in vivo	17072306
TCF7L2	DAXX	NO	in vivo;yeast 2-hybrid	16569639
TCF7L2	CTNNB1	NO	in vitro;in vivo	11713476 , 12861022 , 16306047 , 15684397
TCF7L2	CSNK2A2	NO	in vitro	11711551
TCF7L2	PSEN1	NO	in vitro;in vivo	11504726 , 16306047

Related other genetic factors

Gene related SNPs (count: 103)

Literature-origin SNPs (count: 28)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs12772424	chr10:113120792 - 113120792(1)	intron_variant; upstream_gene_variant	1(1/0/0)
rs290487	chr10:113149972 - 113149972(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs11196224	chr10:113095638 - 113095638(1)	intron_variant	1(0/1/0)
rs7924080	chr10:113027253 - 113027253(1)	intron_variant	1(0/1/0)
rs11196229	chr10:113106413 - 113106413(1)	intron_variant	1(0/1/0)
rs3750804	chr10:113074091 - 113074091(1)	intron_variant	1(0/1/0)
rs7919185	chr10:113130079 - 113130079(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs6585195	chr10:112963195 - 112963195(1)	intron_variant	1(0/1/0)
rs3750805	chr10:113087384 - 113087384(1)	intron_variant	1(1/0/0)
rs7917983	chr10:112973123 - 112973123(1)	intron_variant	1(1/0/0)
rs6585209	chr10:113127429 - 113127429(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs11196201	chr10:113043548 - 113043548(1)	intron_variant	1(0/1/0)
rs7895307	chr10:112984202 - 112984202(1)	intron_variant; upstream_gene_variant	1(1/0/0)
rs4132670	chr10:113008012 - 113008012(1)	intron_variant	1(1/0/0)
rs12184389	chr10:113080011 - 113080011(1)	intron_variant	1(0/1/0)
rs11196203	chr10:113046101 - 113046101(1)	intron_variant	1(0/1/0)
rs10787476	chr10:113139155 - 113139155(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)
rs4309482	chr18:55083238 - 55083238(1)		1(0/1/0)
rs12255372	chr10:113049143 - 113049143(1)	intron_variant	1(0/1/0)
rs9960767	chr18:55487771 - 55487771(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	2(0/2/0)
rs290475	chr10:113114260 - 113114260(1)	intron_variant	1(0/1/0)
rs6585194	chr10:112957712 - 112957712(1)	intron_variant	1(0/1/0)
rs7085532	chr10:113099704 - 113099704(1)	intron_variant	1(0/1/0)
rs1362943	chr10:113128849 - 113128849(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs290484	chr10:113154953 - 113154953(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	1(1/0/0)
rs1885510	chr10:113157683 - 113157683(1)	intron_variant; NMD_transcript_variant; upstream_gene_variant	1(0/1/0)
rs7087006	chr10:113063667 - 113063667(1)	intron_variant	1(0/1/0)
rs11196175	chr10:112976855 - 112976855(1)	intron_variant	1(0/1/0)

LD-proxies (count: 75)

rs_ID	Location	Functional Annotation
rs290477	chr10:113106873 - 113106873(1)	intron_variant
rs290485	chr10:113150161 - 113150161(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10749127	chr10:113089594 - 113089594(1)	intron_variant
rs6585198	chr10:113002478 - 113002478(1)	intron_variant
rs6585197	chr10:113002305 - 113002305(1)	intron_variant
rs10885402	chr10:113001938 - 113001938(1)	intron_variant
rs4074718	chr10:112988858 - 112988858(1)	downstream_gene_variant; intron_variant
rs4074720	chr10:112988738 - 112988738(1)	downstream_gene_variant; intron_variant
rs4639863	chr10:113094624 - 113094624(1)	intron_variant
rs10885405	chr10:113017911 - 113017911(1)	intron_variant
rs10885406	chr10:113017965 - 113017965(1)	intron_variant
rs10787472	chr10:113021538 - 113021538(1)	intron_variant
rs12258200	chr10:113021939 - 113021939(1)	intron_variant
rs6585199	chr10:113005412 - 113005412(1)	intron_variant
rs6585200	chr10:113008850 - 113008850(1)	intron_variant
rs6585201	chr10:113009024 - 113009024(1)	intron_variant
rs7904519	chr10:113014168 - 113014168(1)	intron_variant
rs7100927	chr10:113036289 - 113036289(1)	intron_variant
rs7895340	chr10:113041766 - 113041766(1)	intron_variant
rs11196200	chr10:113042179 - 113042179(1)	intron_variant
rs11196205	chr10:113047288 - 113047288(1)	intron_variant
rs6585202	chr10:113023044 - 113023044(1)	intron_variant
rs7077039	chr10:113029318 - 113029318(1)	intron_variant
rs12359102	chr10:113033692 - 113033692(1)	intron_variant
rs7900150	chr10:113034064 - 113034064(1)	intron_variant
rs7071302	chr10:113057768 - 113057768(1)	intron_variant
rs11196218	chr10:113080735 - 113080735(1)	intron_variant
rs12718338	chr10:113053288 - 113053288(1)	intron_variant
rs12768310	chr10:113079957 - 113079957(1)	intron_variant
rs12265291	chr10:113050481 - 113050481(1)	intron_variant
rs10885409	chr10:113048313 - 113048313(1)	intron_variant
rs966227	chr10:113087007 - 113087007(1)	intron_variant
rs7077247	chr10:113052312 - 113052312(1)	intron_variant
rs11196219	chr10:113080880 - 113080880(1)	intron_variant
rs11196208	chr10:113051557 - 113051557(1)	intron_variant
rs17130183	chr10:113105435 - 113105435(1)	intron_variant
rs7894421	chr10:113102998 - 113102998(1)	intron_variant
rs2296783	chr10:112963891 - 112963891(1)	intron_variant
rs4917644	chr10:113089640 - 113089640(1)	intron_variant
rs3814573	chr10:113138334 - 113138334(1)	intron_variant; non_coding_transcript_variant
rs10787475	chr10:113132709 - 113132709(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs7901275	chr10:112973147 - 112973147(1)	intron_variant
rs11196187	chr10:112999686 - 112999686(1)	intron_variant
rs11196192	chr10:113022528 - 113022528(1)	intron_variant
rs12266632	chr10:113005200 - 113005200(1)	intron_variant
rs7081062	chr10:112980986 - 112980986(1)	intron_variant
rs10128255	chr10:112983076 - 112983076(1)	intron_variant; upstream_gene_variant
rs6585196	chr10:112977291 - 112977291(1)	intron_variant
rs7901695	chr10:112994329 - 112994329(1)	intron_variant
rs7082458	chr10:113086890 - 113086890(1)	intron_variant
rs7079673	chr10:113073868 - 113073868(1)	intron_variant
rs9663295	chr10:113144100 - 113144100(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs12775879	chr10:113144442 - 113144442(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs7074440	chr10:113025665 - 113025665(1)	intron_variant
rs4506565	chr10:112996282 - 112996282(1)	intron_variant
rs7903146	chr10:112998590 - 112998590(1)	intron_variant
rs11196199	chr10:113036358 - 113036358(1)	intron_variant
rs12243326	chr10:113029056 - 113029056(1)	intron_variant
rs2094406	chr10:112954966 - 112954966(1)	intron_variant; upstream_gene_variant
rs7909016	chr10:112957430 - 112957430(1)	intron_variant
rs2094405	chr10:112955930 - 112955930(1)	intron_variant; upstream_gene_variant
rs6585205	chr10:113099405 - 113099405(1)	intron_variant
rs1555485	chr10:113152775 - 113152775(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs11594610	chr10:113153224 - 113153224(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs11594566	chr10:113153211 - 113153211(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs176632	chr10:113151320 - 113151320(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10509970	chr10:113155154 - 113155154(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs290486	chr10:113149980 - 113149980(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs10509969	chr10:113153800 - 113153800(1)	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant
rs4081699	chr10:113160330 - 113160330(1)	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant
rs11196212	chr10:113061490 - 113061490(1)	intron_variant
rs11196213	chr10:113061795 - 113061795(1)	intron_variant
rs4918789	chr10:113062048 - 113062048(1)	intron_variant
rs4917642	chr10:113062190 - 113062190(1)	intron_variant
rs11196174	chr10:112974337 - 112974337(1)	intron_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 2)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 10	chr10:0-133797422	3 (0/2/1)
10q25-q26	chr10:104000000-133797422	2 (0/0/2)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Gene relationship with MDD

View in gBrowse

Region: chr10:112950250..113167678 View in gBrowse