SNP Report

Basic Info

Name	rs10865974 dbSNP Ensembl
Location	chr3:52684264 - 52684264(1)
Variant Alleles	G/T
Ancestral Allele	T
Minor Allele	T
Minor Allele Frequence	0.445487
Functional Annotation	intron_variant; upstream_gene_variant.
Consequence to Transcript	intron_variant(ENST00000394830, ENST00000420148, ENST00000424867, ENST00000431678, ENST00000439181, ENST00000449505, ENST00000450271, ENST00000458294, ENST00000479230); upstream_gene_variant(ENST00000296302, ENST00000337303, ENST00000356770, ENST00000391191, ENST00000394799, ENST00000409057, ENST00000409114, ENST00000409767, ENST00000410007, ENST00000412587, ENST00000418458, ENST00000423351, ENST00000460073, ENST00000462550, ENST00000468146, ENST00000468885, ENST00000474423, ENST00000484022, ENST00000492349, ENST00000496254, ENST00000516978, ENST00000630615)
No. of Studies	1 (Positive: 0; Negative: 0; Trend: 1)
Source	Literature
Overlap with SZ?	NO
Overlap with MDD?	NO

SNP related studies (count: 1)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Goes, F. S.,2012		T	OR = 0.84,P-value(Meta) = 0.00000218 OR = 0.84,P-value(Meta) = 0.00000218	Suggestive association was found. Suggestive association was found.	Trend

SNP related genes (count: 3)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
SNORD19	small nucleolar RNA, C/D box 19	3p21.1	Mapped by Literature SNP
GNL3	guanine nucleotide binding protein-like 3 (nucleolar)	3p21.1	2(2/0/0)
PBRM1	polybromo 1	3p21	5(4/0/1)

SNPs in LD with rs10865974 (count: 125) View in gBrowse (chr3:52502498..52799789 )

The LD data used here is based on HapMap rel#27. LD SNP pairs were selected with a threshold r²<=0.8.

Literature-origin SNPs (count: 0)

LD-proxies (count: 125)

rs_ID	Functional Annotation	r²[population]
rs13082960	intron_variant; NMD_transcript_variant; upstream_gene_variant	0.952[CHB]; 0.976[CHD]; 1.0[JPT]
rs11711421	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.953[JPT]
rs6762813	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2071506	downstream_gene_variant; upstream_gene_variant	0.86[JPT]
rs2336146	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1010553	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.822[CHB]; 0.813[CHD]
rs6786043	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs6617	5_prime_UTR_variant; downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs2019065	upstream_gene_variant	0.83[CHB]; 0.909[JPT]
rs2268025	intron_variant	1.0[CHB]; 1.0[JPT]
rs3617	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.822[CHB]
rs11130312	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs4282054	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.882[CHD]; 0.953[JPT]
rs17052259	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs3774365	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs4687551	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.815[JPT]
rs4687638	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2336545	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs10510760	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2239699	downstream_gene_variant; upstream_gene_variant	0.836[JPT]
rs3796353	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs998909	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs1014969	upstream_gene_variant	1.0[CHB]; 0.903[CHD]; 1.0[JPT]
rs2159644	downstream_gene_variant; intron_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs8906	5_prime_UTR_variant; downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs6445528	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.951[CHD]; 1.0[JPT]
rs2239551	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs12488461	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.955[CHB]; 0.952[CHD]; 0.907[JPT]
rs2230535	downstream_gene_variant; synonymous_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs6804145	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4687548	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs4475032	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.951[CHD]; 1.0[JPT]
rs11235	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	0.952[CHB]; 0.834[JPT]
rs2240919	downstream_gene_variant; intron_variant; upstream_gene_variant	0.856[JPT]
rs34017441	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 0.976[CHD]; 0.953[JPT]
rs11130310	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 0.907[JPT]
rs3755798	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 1.0[CHD]; 1.0[JPT]
rs13063160	intron_variant; NMD_transcript_variant	0.953[CHB]; 0.951[CHD]; 0.953[JPT]
rs2276824	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.909[JPT]
rs3852066	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1866268	intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs3733045	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1133415	3_prime_UTR_variant; downstream_gene_variant; intron_variant	0.908[CHB]; 0.927[CHD]; 1.0[JPT]
rs6778844	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs6786919	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 0.953[JPT]
rs2268027	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs3733039	intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2071508	downstream_gene_variant; upstream_gene_variant	0.86[JPT]
rs2083180	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs6445535	downstream_gene_variant; intron_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs6778735	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.882[CHD]; 0.953[JPT]
rs13081028	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.864[CHB]; 0.86[CHD]
rs2164884	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[JPT]
rs11130323	downstream_gene_variant; intron_variant	1.0[CHB]; 1.0[JPT]
rs4687550	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs9879090	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.909[JPT]
rs13071584	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.952[CHD]; 1.0[JPT]
rs1075653	downstream_gene_variant; intron_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant	0.86[JPT]
rs11720159	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.938[JPT]
rs10865973	intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs11717836	upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs6798246	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs13303	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.955[CHB]; 0.86[CHD]; 0.909[JPT]
rs2878628	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.952[CHD]; 1.0[JPT]
rs10780035	intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs1961959	downstream_gene_variant; intron_variant; NMD_transcript_variant	0.911[CHB]; 1.0[JPT]
rs13083798	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.927[CHD]; 0.907[JPT]
rs11716747	downstream_gene_variant; intron_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs6778329	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.9[JPT]
rs2577831	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.928[CHD]; 0.909[JPT]
rs17052256	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs1076425	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs9881468	downstream_gene_variant; upstream_gene_variant	0.86[JPT]
rs7652191	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs1108842	5_prime_UTR_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 0.929[CHD]; 0.909[JPT]
rs7624716	intron_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs11720243	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs13085775	intron_variant; NMD_transcript_variant	0.907[CHB]; 0.928[CHD]; 0.909[JPT]
rs11177	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 0.953[JPT]
rs2590838	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.929[CHD]; 0.909[JPT]
rs2028216	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs35526119	downstream_gene_variant; intron_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2239549	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs7638808	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.951[CHD]; 1.0[JPT]
rs4687626	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.951[CHD]; 1.0[JPT]
rs678	downstream_gene_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.909[JPT]
rs1029871	downstream_gene_variant; missense_variant	1.0[CHB]; 1.0[JPT]
rs12487445	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.951[CHD]; 1.0[JPT]
rs9853056	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.864[CHB]; 0.858[CHD]
rs3774366	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs4687629	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs7614981	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.953[CHB]; 0.882[CHD]; 0.953[JPT]
rs731831	downstream_gene_variant; intron_variant; non_coding_transcript_variant	0.818[CHB]; 0.854[CHD]
rs9324	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant	0.86[JPT]
rs3774355	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.815[JPT]
rs2300149	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs2079929	intron_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs12497998	downstream_gene_variant; intron_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs6445534	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 0.953[JPT]
rs2270197	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs6805156	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs3774354	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs2071507	downstream_gene_variant; upstream_gene_variant	0.909[JPT]
rs6976	3_prime_UTR_variant; downstream_gene_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2286798	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.909[JPT]
rs1010552	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.844[CHB]
rs2072390	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2268023	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.86[JPT]
rs1961958	downstream_gene_variant; intron_variant; NMD_transcript_variant; upstream_gene_variant	0.955[CHB]; 0.952[CHD]; 0.953[JPT]
rs13085895	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[JPT]
rs12489828	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.95[CHB]; 0.947[JPT]
rs4687625	intron_variant; NMD_transcript_variant; non_coding_transcript_variant; upstream_gene_variant	0.951[CHB]; 1.0[JPT]
rs13082208	intron_variant; NMD_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[JPT]
rs2289249	downstream_gene_variant; intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 0.953[JPT]
rs11714419	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs7622694	intron_variant; NMD_transcript_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs11714565	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.976[CHD]; 1.0[JPT]
rs2164885	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 0.952[JPT]
rs2118540	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	1.0[CHB]; 0.95[JPT]
rs767418	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs2240920	downstream_gene_variant; intron_variant; upstream_gene_variant	0.909[JPT]
rs17264436	3_prime_UTR_variant; intron_variant; NMD_transcript_variant; synonymous_variant	1.0[CHB]; 1.0[JPT]
rs13079063	3_prime_UTR_variant; downstream_gene_variant; upstream_gene_variant	1.0[CHB]; 0.95[CHD]; 0.952[JPT]
rs3733041	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]
rs12635140	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant	1.0[CHB]; 1.0[CHD]; 1.0[JPT]

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with MDD from cross-disorder studies (count: 0)