SNP Report

Basic Info

Name	rs2235349 dbSNP Ensembl
Location	chr22:50079810 - 50079810(1)
Variant Alleles	T/C
Ancestral Allele	T
Minor Allele	C
Minor Allele Frequence	0.242812
Functional Annotation	intron_variant.
Consequence to Transcript	intron_variant(ENST00000311597, ENST00000395876, ENST00000442311)
No. of Studies	2 (Positive: 1; Negative: 1; Trend: 0)
Source	Literature
Overlap with SZ?	YES
Overlap with MDD?	NO

SNP related studies (count: 2)

Reference	Allele Change	Risk Allele	Statistical Values	Author Comments	Result Category
Verma, R.,2005(b)	A/G		Case-control association: for BPAD, Fisher exact test, allel...... Case-control association: for BPAD, Fisher exact test, allele P-value > 0.05; chi-square test, genotype P-value(additive)>0.05, P-value(dominant)>0.05, P-value(recessive)>0.05 ; Family-Based Association: for BPAD, TDT, P-value = 0.02, minor allele T/NT: 48/27 More...	Significant association was observed in family based associa...... Significant association was observed in family based association analysis. More...	Positive
Selch, S., 2007	C/T		chi-square tests, P-value > 0.05 chi-square tests, P-value > 0.05	No association with the combined patient sample or BPD was f...... No association with the combined patient sample or BPD was found. More...	Negative

SNP related genes (count: 1)

Approved Symbol	Approved Name	Location	No. of Studies (Positive/Negative/Trend)
MLC1	megalencephalic leukoencephalopathy with subcortical cysts 1	22q13.33	5(1/4/0)

SNPs in LD with rs2235349 (count: 68) View in gBrowse (chr22:50072945..50150279 )

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: 68)

rs_ID	Functional Annotation	r²[population]
rs4838809	intron_variant; NMD_transcript_variant	0.867[CEU]; 1.0[CHB]
rs2015453	intron_variant; upstream_gene_variant	0.827[CEU]; 1.0[CHB]; 0.827[JPT]
rs715619	intron_variant; NMD_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs13058004	intron_variant; upstream_gene_variant	0.868[CEU]
rs13055917	intron_variant; NMD_transcript_variant	0.824[CEU]; 1.0[CHB]; 0.827[JPT]
rs2340602	intron_variant; NMD_transcript_variant	0.837[CEU]; 1.0[CHB]; 0.838[JPT]
rs9617036	intron_variant; NMD_transcript_variant	0.887[CEU]; 1.0[CHB]; 0.827[JPT]
rs138209	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.809[CHB]
rs4838830	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.827[CEU]; 0.948[CHB]; 0.827[JPT]
rs4838807	intron_variant; NMD_transcript_variant	0.875[CEU]; 1.0[CHB]; 0.838[JPT]
rs2142850	intron_variant; NMD_transcript_variant	0.867[CEU]; 1.0[CHB]; 0.827[JPT]
rs4838820	upstream_gene_variant	1.0[CEU]; 0.948[CHB]; 0.827[JPT]
rs9617066	3_prime_UTR_variant; missense_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	0.915[CEU]; 0.95[CHB]; 0.838[JPT]
rs2272835	downstream_gene_variant; intron_variant; upstream_gene_variant	0.827[CEU]; 0.901[CHB]
rs8138886	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs17836601	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs9617086	intron_variant; NMD_transcript_variant	0.863[CEU]; 0.948[CHB]; 0.835[JPT]
rs4838823	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.913[CEU]; 0.948[CHB]; 0.827[JPT]
rs138228	intron_variant; NMD_transcript_variant	0.896[CHB]
rs11101949	downstream_gene_variant; intron_variant; upstream_gene_variant	0.83[CEU]; 1.0[CHB]
rs2142851	intron_variant; NMD_transcript_variant	0.875[CEU]; 1.0[CHB]; 0.838[JPT]
rs732449	downstream_gene_variant; intron_variant; upstream_gene_variant	0.837[CEU]; 1.0[CHB]; 0.838[JPT]
rs7285511	intron_variant; non_coding_transcript_variant; upstream_gene_variant	0.809[CHB]
rs9617024	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.867[CEU]; 0.948[CHB]; 0.827[JPT]
rs760750	downstream_gene_variant; intron_variant; upstream_gene_variant	0.818[CEU]; 1.0[CHB]; 0.826[JPT]
rs2340599	intron_variant; NMD_transcript_variant	0.91[CEU]; 1.0[CHB]; 0.838[JPT]
rs4838811	5_prime_UTR_variant; downstream_gene_variant; intron_variant; upstream_gene_variant	0.827[CEU]; 1.0[CHB]; 0.827[JPT]
rs138226	intron_variant; NMD_transcript_variant	0.891[CHB]; 0.828[JPT]
rs138244	intron_variant; NMD_transcript_variant	0.862[CHB]
rs4838831	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.862[CEU]; 0.948[CHB]; 0.827[JPT]
rs4838816	intron_variant; upstream_gene_variant	0.8[CHB]
rs12484523	intron_variant	1.0[CEU]; 1.0[CHB]; 0.946[JPT]
rs9617070	intron_variant; NMD_transcript_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs138240	intron_variant; NMD_transcript_variant	0.949[CHB]
rs9617105	downstream_gene_variant; intron_variant; upstream_gene_variant	0.829[CEU]; 0.896[CHB]
rs138249	intron_variant; NMD_transcript_variant	0.857[CHB]
rs2340603	intron_variant; NMD_transcript_variant	0.837[CEU]; 1.0[CHB]
rs9617083	intron_variant; NMD_transcript_variant	0.912[CEU]; 0.95[CHB]; 0.838[JPT]
rs4240525	intron_variant; upstream_gene_variant	0.867[CEU]; 0.948[CHB]; 0.827[JPT]
rs4838849	intron_variant; NMD_transcript_variant	0.837[CEU]; 1.0[CHB]; 0.838[JPT]
rs2340597	intron_variant; upstream_gene_variant	0.913[CEU]; 0.948[CHB]; 0.827[JPT]
rs2235350	intron_variant	1.0[CEU]; 1.0[CHB]; 0.946[JPT]
rs2294395	intron_variant	0.901[CHB]; 0.838[JPT]
rs2340601	3_prime_UTR_variant; missense_variant; NMD_transcript_variant	0.866[CEU]; 1.0[CHB]
rs3736690	intron_variant; NMD_transcript_variant	0.833[CEU]; 1.0[CHB]; 0.838[JPT]
rs9617095	intron_variant; NMD_transcript_variant	0.865[CEU]; 1.0[CHB]; 0.815[JPT]
rs4838828	downstream_gene_variant; intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs138232	intron_variant; NMD_transcript_variant	0.947[CHB]
rs2272836	downstream_gene_variant; missense_variant; synonymous_variant; upstream_gene_variant	0.898[CHB]; 0.827[JPT]
rs742183	intron_variant; NMD_transcript_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs4838839	intron_variant; upstream_gene_variant	0.867[CEU]; 0.948[CHB]; 0.827[JPT]
rs4838843	intron_variant; NMD_transcript_variant	0.837[CEU]; 1.0[CHB]; 0.838[JPT]
rs9617100	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.835[JPT]
rs9617097	intron_variant; NMD_transcript_variant	1.0[CHB]; 0.838[JPT]
rs84504	intron_variant; NMD_transcript_variant	0.896[CHB]
rs3810974	downstream_gene_variant; intron_variant	0.867[CEU]; 0.948[CHB]; 0.827[JPT]
rs3810972	downstream_gene_variant; intron_variant	0.875[CEU]; 0.95[CHB]; 0.838[JPT]
rs760751	intron_variant; upstream_gene_variant	1.0[CHB]
rs5771362	intron_variant; upstream_gene_variant	0.873[CEU]; 1.0[CHB]; 0.943[JPT]
rs138238	intron_variant; NMD_transcript_variant	0.857[CHB]
rs4838832	intron_variant; NMD_transcript_variant; non_coding_transcript_variant	0.867[CEU]; 0.948[CHB]
rs13053780	intron_variant	1.0[CEU]; 1.0[CHB]; 0.89[JPT]
rs3736691	intron_variant; NMD_transcript_variant	0.875[CEU]; 1.0[CHB]; 0.838[JPT]
rs3810973	downstream_gene_variant; intron_variant	0.867[CEU]; 0.948[CHB]; 0.827[JPT]
rs9617062	intron_variant	1.0[CEU]; 1.0[CHB]; 0.943[JPT]
rs2015446	intron_variant; upstream_gene_variant	0.827[CEU]; 1.0[CHB]; 0.827[JPT]
rs4838845	intron_variant; NMD_transcript_variant	0.851[CEU]
rs2272838	downstream_gene_variant; synonymous_variant; upstream_gene_variant	0.827[CEU]; 1.0[CHB]; 0.827[JPT]

Overlap with SZ from cross-disorder studies (count: 2)

Reference	Statistical Result	Description	Result Category
Selch, S., 2007	chi-square tests, P-value > 0.05	No association with the combined patient sample, SCZ or type A or type B schizophrenia was found.	Negative
Verma, R.,2005(b)	Case-control association:for SCZ, Fisher exact test, allele P-value = 0.03; chi-square test, genotype P-value(additive)=0.02, P-value(dominant)=0.006, P-value(recessive)>0.05;Family-Based Association:for SCZ, TDT, P-value > 0.05	Significant association was observed in case-control association analysis.	Positive

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