Variant report

Variant	rs9871957
Chromosome Location	chr3:78982662-78982663
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1031933	1.00[CHD][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap]
rs10511125	1.00[CEU][hapmap]
rs10511126	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs13317939	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13322089	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13325291	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1480685	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1480686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162819	1.00[CEU][hapmap]
rs162873	1.00[CEU][hapmap]
rs162875	1.00[CEU][hapmap]
rs167944	1.00[CEU][hapmap]
rs17016495	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs17016507	1.00[CEU][hapmap]
rs17016511	1.00[CEU][hapmap]
rs17016573	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17016593	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17016646	0.91[YRI][hapmap]
rs17016656	1.00[CHD][hapmap]
rs2125123	1.00[CEU][hapmap]
rs2271575	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28431826	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28611062	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331132	1.00[CEU][hapmap]
rs331133	1.00[CEU][hapmap]
rs331159	1.00[CEU][hapmap]
rs333499	1.00[CEU][hapmap]
rs58608513	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59931439	0.92[EUR][1000 genomes]
rs72904273	0.92[EUR][1000 genomes]
rs72904277	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906141	0.92[EUR][1000 genomes]
rs9631526	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9822620	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9829918	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9832632	1.00[CHD][hapmap]
rs9835586	1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836486	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839144	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9842144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9845223	0.84[YRI][hapmap]
rs9861490	0.90[YRI][hapmap]
rs9868575	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876637	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880690	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834744	chr3:78911545-79076470	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv470672	chr3:78913203-78985805	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv590734	chr3:78915205-78985805	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78959600-78987200	Weak transcription	Fetal Lung	lung
2	chr3:78963200-78991000	Weak transcription	Fetal Brain Male	brain
3	chr3:78967200-78987200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:78967200-79000600	Weak transcription	Fetal Kidney	kidney
5	chr3:78968800-78987200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:78969000-78990800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:78969000-78991000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:78969200-78990400	Weak transcription	NHEK	skin
9	chr3:78969600-79000600	Weak transcription	HepG2	liver
10	chr3:78970400-78991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:78975600-78987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:78977200-78990800	Weak transcription	Psoas Muscle	Psoas
13	chr3:78977400-78987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:78977400-78987200	Weak transcription	Fetal Stomach	stomach
15	chr3:78978400-78992200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:78978800-78990800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:78979600-78987000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:78979600-78987200	Weak transcription	Aorta	Aorta
19	chr3:78980600-78989400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:78981600-78991600	Weak transcription	Fetal Heart	heart
21	chr3:78982400-78983600	Weak transcription	Brain Angular Gyrus	brain
22	chr3:78982400-79001800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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