Variant report

Variant	rs11631339
Chromosome Location	chr15:33097894-33097895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10519756	1.00[LWK][hapmap]
rs11629595	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631977	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632555	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635639	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636339	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853746	1.00[JPT][hapmap]
rs12148284	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148371	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12442768	1.00[JPT][hapmap]
rs12898616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901405	1.00[JPT][hapmap]
rs12906330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911544	1.00[JPT][hapmap]
rs17228641	1.00[LWK][hapmap]
rs17816333	1.00[JPT][hapmap]
rs17816345	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17816387	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123068	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339158	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62002618	0.90[AFR][1000 genomes]
rs7178265	1.00[LWK][hapmap];0.94[MKK][hapmap]
rs9806641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422296	chr15:32798938-33221215	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv482680	chr15:32958401-33154005	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv832961	chr15:33021177-33134988	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv903977	chr15:33040782-33117302	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv1482	chr15:33083166-33113644	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11631339	GABRG3	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33061200-33141000	Weak transcription	Placenta	Placenta
2	chr15:33062600-33111200	Weak transcription	Gastric	stomach
3	chr15:33065800-33098600	Weak transcription	Colonic Mucosa	Colon
4	chr15:33088800-33107800	Weak transcription	Stomach Mucosa	stomach
5	chr15:33094800-33100800	Weak transcription	Fetal Kidney	kidney
6	chr15:33096200-33101400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:33096200-33111000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr15:33096200-33111000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:33096200-33154000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:33096400-33098800	Weak transcription	Pancreas	Pancrea
11	chr15:33096400-33100600	Weak transcription	Brain Angular Gyrus	brain
12	chr15:33096400-33104000	Weak transcription	Aorta	Aorta
13	chr15:33096400-33105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:33096400-33109600	Weak transcription	Osteobl	bone
15	chr15:33096400-33110800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:33096400-33111000	Weak transcription	NHLF	lung
17	chr15:33096400-33111400	Weak transcription	HSMMtube	muscle
18	chr15:33096400-33116200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:33096400-33159000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:33096600-33098000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:33096600-33103000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:33096600-33104400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:33097800-33100200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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