Variant report

Variant	rs9643820
Chromosome Location	chr8:54686687-54686688
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr8:54686458-54686880	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF143	chr8:54686650-54686691	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:54685269..54687285-chr8:54688387..54691070,4	K562	blood:
2	chr8:54685671..54687300-chr8:54728905..54731468,2	MCF-7	breast:
3	chr8:54685641..54687590-chr8:54702056..54704049,2	K562	blood:
4	chr8:54685432..54687285-chr8:54688902..54690630,2	K562	blood:

Variant related genes	Relation type
ATP6V1H	TF binding region
ENSG00000047249	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1031979	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1031980	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10435587	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11994467	0.85[ASN][1000 genomes]
rs11996300	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12056486	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12056719	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12115070	0.84[EUR][1000 genomes]
rs12234972	0.85[CEU][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13276766	0.82[ASN][1000 genomes]
rs1552148	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16919507	1.00[CEU][hapmap]
rs16919508	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16919522	1.00[CEU][hapmap];0.91[ASN][1000 genomes]
rs16919534	1.00[CEU][hapmap];0.91[ASN][1000 genomes]
rs16919537	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16919541	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16919563	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16919571	1.00[CEU][hapmap];0.95[ASN][1000 genomes]
rs16919573	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1872063	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1905061	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2128150	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2170444	1.00[CEU][hapmap];0.96[ASN][1000 genomes]
rs2376011	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3735831	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757954	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3824121	0.82[YRI][hapmap]
rs41321146	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4236945	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4737192	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4737518	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4737554	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4737558	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4737761	0.87[CEU][hapmap]
rs4737764	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4737765	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737821	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4737974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs4738025	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs4738027	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs4738470	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4738646	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4738701	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4738884	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4738916	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55682919	0.82[EUR][1000 genomes]
rs55876329	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs55964335	0.93[ASN][1000 genomes]
rs56818292	0.87[ASN][1000 genomes]
rs56956173	0.92[EUR][1000 genomes]
rs56973376	0.93[ASN][1000 genomes]
rs57071607	1.00[EUR][1000 genomes]
rs57550901	0.82[EUR][1000 genomes]
rs58473841	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58558817	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58970885	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61070518	0.85[ASN][1000 genomes]
rs6473893	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs6984257	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6986372	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6987427	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6988009	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6988082	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6988808	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6988812	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6994851	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6997003	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6997127	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6998532	0.82[YRI][hapmap]
rs6999454	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs7005696	1.00[CEU][hapmap]
rs7006934	0.87[CEU][hapmap]
rs7009705	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7018162	1.00[CEU][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73587624	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73587627	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73680316	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73680321	0.92[EUR][1000 genomes]
rs73682552	0.82[EUR][1000 genomes]
rs73682555	0.91[ASN][1000 genomes]
rs73682568	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73682570	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7387704	0.86[AMR][1000 genomes]
rs7843701	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs900163	1.00[CEU][hapmap];0.91[ASN][1000 genomes]
rs958268	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9643480	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9643819	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758159	chr8:54474589-54737473	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv2759616	chr8:54474589-54737473	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1021775	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv539621	chr8:54631303-54827173	Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54650200-54707400	Weak transcription	HUVEC	blood vessel
2	chr8:54655400-54703600	Weak transcription	Brain Angular Gyrus	brain
3	chr8:54655800-54726000	Weak transcription	Colonic Mucosa	Colon
4	chr8:54667800-54687400	Weak transcription	Spleen	Spleen
5	chr8:54667800-54726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:54668000-54687400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr8:54668000-54703000	Weak transcription	Brain Substantia Nigra	brain
8	chr8:54669400-54687400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr8:54671200-54687000	Weak transcription	Fetal Brain Male	brain
10	chr8:54673000-54687400	Weak transcription	Small Intestine	intestine
11	chr8:54673200-54687400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr8:54673400-54687400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr8:54673400-54687600	Weak transcription	Esophagus	oesophagus
14	chr8:54673400-54687600	Weak transcription	Lung	lung
15	chr8:54673400-54698200	Weak transcription	Pancreas	Pancrea
16	chr8:54673400-54698400	Weak transcription	Gastric	stomach
17	chr8:54673400-54703000	Weak transcription	Left Ventricle	heart
18	chr8:54673400-54704000	Weak transcription	Right Ventricle	heart
19	chr8:54673600-54691200	Weak transcription	HepG2	liver
20	chr8:54675200-54689000	Weak transcription	Fetal Heart	heart
21	chr8:54676600-54686800	Weak transcription	Brain Hippocampus Middle	brain
22	chr8:54676600-54702800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr8:54676600-54703200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr8:54676600-54703800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr8:54677600-54687400	Weak transcription	Fetal Stomach	stomach
26	chr8:54680800-54687400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr8:54681000-54687000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr8:54681000-54689000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr8:54681000-54707400	Weak transcription	NHLF	lung
30	chr8:54681000-54726200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:54681200-54687200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr8:54681200-54704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:54681200-54707400	Weak transcription	Hela-S3	cervix
34	chr8:54681400-54686800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr8:54681400-54686800	Weak transcription	A549	lung
36	chr8:54681400-54687800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr8:54681400-54691200	Weak transcription	Stomach Mucosa	stomach
38	chr8:54681400-54699000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr8:54681400-54703200	Weak transcription	NHEK	skin
40	chr8:54681400-54703800	Weak transcription	HMEC	breast
41	chr8:54681400-54707600	Weak transcription	NH-A	brain
42	chr8:54681800-54687600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr8:54681800-54687600	Weak transcription	Brain Germinal Matrix	brain
44	chr8:54682000-54687200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr8:54682000-54687200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr8:54682000-54690400	Weak transcription	K562	blood
47	chr8:54682200-54687400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr8:54682200-54698200	Weak transcription	Fetal Kidney	kidney
49	chr8:54682200-54703800	Weak transcription	Brain Anterior Caudate	brain
50	chr8:54682400-54686800	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links