Variant report

Variant	rs17456385
Chromosome Location	chr6:128626631-128626632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10428737	0.87[GIH][hapmap]
rs11964875	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11965122	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs11965141	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11966128	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs1339189	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1339196	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1416517	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1538498	1.00[EUR][1000 genomes]
rs1612415	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs17055564	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17055574	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17055596	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17055597	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17055601	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17055604	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055608	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055611	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17055612	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs17055616	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055617	0.84[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs17055618	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17055619	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs17055628	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17055630	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17055679	1.00[EUR][1000 genomes]
rs17055689	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17055706	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055717	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs17055719	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17055727	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17055733	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17055854	0.87[GIH][hapmap]
rs17343887	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[EUR][1000 genomes]
rs17353545	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17430131	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17430452	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17456343	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17456601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1768360	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2027311	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs4267969	1.00[EUR][1000 genomes]
rs4466261	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs55700986	0.85[EUR][1000 genomes]
rs55969073	1.00[EUR][1000 genomes]
rs56095177	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56241890	1.00[EUR][1000 genomes]
rs57318936	1.00[EUR][1000 genomes]
rs59132771	1.00[EUR][1000 genomes]
rs60915390	0.81[EUR][1000 genomes]
rs6420738	0.91[EUR][1000 genomes]
rs6913718	0.98[EUR][1000 genomes]
rs6931769	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs6933821	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs72967021	0.85[EUR][1000 genomes]
rs72967026	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967039	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967046	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967053	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72967056	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72967058	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72967074	1.00[EUR][1000 genomes]
rs72967078	0.98[EUR][1000 genomes]
rs72967081	0.98[EUR][1000 genomes]
rs72967087	0.98[EUR][1000 genomes]
rs72967090	0.98[EUR][1000 genomes]
rs72969051	0.91[EUR][1000 genomes]
rs72969054	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969059	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969061	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969063	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969067	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969070	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969074	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72969075	0.98[EUR][1000 genomes]
rs72969078	0.98[EUR][1000 genomes]
rs72969081	0.91[EUR][1000 genomes]
rs72969088	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72969090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72969093	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72969097	1.00[EUR][1000 genomes]
rs72969098	0.98[EUR][1000 genomes]
rs72971103	1.00[EUR][1000 genomes]
rs72971104	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72972078	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72972082	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72972084	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72972086	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72972090	0.89[EUR][1000 genomes]
rs72972091	0.91[EUR][1000 genomes]
rs72974006	0.84[AFR][1000 genomes]
rs7764930	1.00[GIH][hapmap]
rs7771630	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7773248	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs7776405	1.00[EUR][1000 genomes]
rs9321114	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs9375562	0.85[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs9402035	0.92[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9491939	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv970667	chr6:128622520-128630617	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128593000-128631600	Weak transcription	Left Ventricle	heart
2	chr6:128602400-128632400	Weak transcription	Pancreas	Pancrea
3	chr6:128603000-128642800	Weak transcription	Fetal Intestine Large	intestine
4	chr6:128604400-128630600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:128604400-128633200	Weak transcription	Fetal Thymus	thymus
6	chr6:128605800-128627400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:128605800-128631200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:128606200-128630600	Weak transcription	Fetal Heart	heart
9	chr6:128609000-128646000	Weak transcription	NH-A	brain
10	chr6:128610800-128643200	Weak transcription	NHEK	skin
11	chr6:128612800-128630400	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:128613200-128640800	Weak transcription	HepG2	liver
13	chr6:128621800-128649000	Weak transcription	HSMMtube	muscle
14	chr6:128622200-128628800	Weak transcription	NHDF-Ad	bronchial
15	chr6:128622200-128631400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:128625200-128642600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:128625400-128627000	Weak transcription	HSMM	muscle
18	chr6:128626000-128629400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:128626000-128631800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:128626000-128643000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:128626200-128631600	Weak transcription	Lung	lung
22	chr6:128626200-128645800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr6:128626400-128626800	Enhancers	HUVEC	blood vessel
24	chr6:128626600-128641400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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