Variant report

Variant	rs9806641
Chromosome Location	chr15:33095895-33095896
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11629595	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631339	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]
rs11631977	0.84[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632555	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635639	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636339	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853746	1.00[JPT][hapmap]
rs12148284	0.92[AMR][1000 genomes];0.86[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	0.95[AMR][1000 genomes];1.00[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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911544	1.00[JPT][hapmap]
rs17816333	1.00[JPT][hapmap]
rs17816345	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs17816387	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123068	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339158	0.92[AMR][1000 genomes];0.86[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
rs9806641	GABRG3	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33060600-33097600	Weak transcription	Thymus	Thymus
2	chr15:33061200-33141000	Weak transcription	Placenta	Placenta
3	chr15:33062600-33111200	Weak transcription	Gastric	stomach
4	chr15:33065800-33098600	Weak transcription	Colonic Mucosa	Colon
5	chr15:33075000-33096400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:33082600-33096000	Weak transcription	Pancreas	Pancrea
7	chr15:33083600-33097400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:33086400-33096000	Weak transcription	Fetal Thymus	thymus
9	chr15:33087600-33096000	Weak transcription	Brain Angular Gyrus	brain
10	chr15:33088800-33107800	Weak transcription	Stomach Mucosa	stomach
11	chr15:33091000-33096600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:33094800-33100800	Weak transcription	Fetal Kidney	kidney
13	chr15:33095000-33096200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:33095200-33096400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:33095200-33096400	ZNF genes & repeats	HSMM	muscle
16	chr15:33095400-33096200	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr15:33095400-33096400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:33095400-33096400	ZNF genes & repeats	Osteobl	bone
19	chr15:33095400-33096600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:33095600-33096000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:33095600-33096000	ZNF genes & repeats	A549	lung
22	chr15:33095600-33096000	ZNF genes & repeats	NHDF-Ad	bronchial
23	chr15:33095600-33096200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:33095600-33096200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:33095600-33096200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:33095600-33096200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
27	chr15:33095600-33096400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:33095600-33096400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:33095600-33096400	ZNF genes & repeats	Aorta	Aorta
30	chr15:33095600-33096400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
31	chr15:33095600-33096400	ZNF genes & repeats	HSMMtube	muscle
32	chr15:33095600-33096400	ZNF genes & repeats	NHLF	lung
33	chr15:33095600-33096600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr15:33095600-33096600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr15:33095800-33096200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:33095800-33096200	ZNF genes & repeats	Lung	lung
37	chr15:33095800-33096200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
38	chr15:33095800-33096400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:33095800-33096400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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