Variant report

Variant	rs6963498
Chromosome Location	chr7:50855509-50855510
allele	C/T
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	POLR2A	chr7:50854387-50857396	A549	lung:	n/a	n/a
2	REST	chr7:50855486-50855990	HL-60	blood:	n/a	chr7:50855727-50855740 chr7:50855732-50855752 chr7:50855742-50855751 chr7:50855732-50855746 chr7:50855734-50855744 chr7:50855724-50855737
3	POLR2A	chr7:50855252-50855552	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:50855206-50855519	MCF-7	breast:	n/a	n/a
5	POLR2A	chr7:50854537-50861857	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50855414..50858546-chr7:50859457..50861249,3	MCF-7	breast:
2	chr7:50763398..50765594-chr7:50855405..50857428,2	K562	blood:

Variant related genes	Relation type
GRB10	TF binding region
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1014384	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1015573	0.83[ASN][1000 genomes]
rs1019000	0.84[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes]
rs10226937	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10231012	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10235345	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10239268	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1024531	0.86[AMR][1000 genomes]
rs10248029	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258458	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10264904	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10268643	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10273302	0.93[CEU][hapmap];0.85[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10276986	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10278363	0.83[CEU][hapmap]
rs10281065	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10464765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464766	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464790	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486761	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238310	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238311	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238313	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238315	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11238325	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238337	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238339	0.94[CEU][hapmap];0.85[JPT][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763072	0.85[JPT][hapmap]
rs11974751	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11978750	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11983539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665949	0.93[CEU][hapmap]
rs12671577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12674028	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718925	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718926	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718927	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718930	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232029	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13311390	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs1859571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051895	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074719	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074720	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074721	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074722	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074777	0.85[JPT][hapmap]
rs2158670	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286152	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2286154	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2329554	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876846	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801000	0.86[AMR][1000 genomes]
rs4947861	0.83[CEU][hapmap]
rs6593164	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6593173	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6593174	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6593182	0.88[CEU][hapmap]
rs6593200	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6943153	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6943901	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945597	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6946194	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6951356	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6957007	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6960912	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6966774	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971834	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6979369	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs734422	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs757773	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757774	0.81[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757777	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757778	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785908	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7785914	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7786917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7788511	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791286	0.91[GIH][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs7793570	0.84[JPT][hapmap]
rs7802338	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809623	0.81[AMR][1000 genomes]
rs886700	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv824091	chr7:50828682-50885984	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538835	chr7:50839656-50867735	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv824092	chr7:50846084-50865531	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6963498	LOC100129427	cis	parietal	SCAN
rs6963498	VWC2	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50850800-50858600	Weak transcription	Aorta	Aorta
2	chr7:50851000-50856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:50851000-50859000	Weak transcription	NHLF	lung
4	chr7:50851200-50855600	Weak transcription	Primary T cells from cord blood	blood
5	chr7:50851200-50857000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:50851400-50857800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:50851400-50858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr7:50851600-50856000	Weak transcription	A549	lung
9	chr7:50851600-50857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:50851600-50857600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:50851600-50857800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr7:50851600-50858200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr7:50851600-50858200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:50851600-50859000	Weak transcription	Osteobl	bone
15	chr7:50852000-50858200	Weak transcription	Fetal Lung	lung
16	chr7:50852200-50858200	Weak transcription	HSMMtube	muscle
17	chr7:50852400-50856200	Weak transcription	Colon Smooth Muscle	Colon
18	chr7:50852600-50857600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:50852800-50856200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:50853000-50857800	Weak transcription	NH-A	brain
21	chr7:50853400-50858200	Enhancers	Pancreas	Pancrea
22	chr7:50853400-50859800	Weak transcription	Gastric	stomach
23	chr7:50854400-50855600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr7:50854400-50856400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr7:50854400-50856800	Enhancers	Right Atrium	heart
26	chr7:50854600-50856800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:50854600-50857800	Enhancers	HUVEC	blood vessel
28	chr7:50854800-50855800	ZNF genes & repeats	Esophagus	oesophagus
29	chr7:50854800-50856600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr7:50854800-50857800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:50854800-50857800	Enhancers	Left Ventricle	heart
32	chr7:50854800-50858200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:50854800-50858200	Enhancers	Lung	lung
34	chr7:50855000-50857200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:50855200-50855600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr7:50855200-50855800	Enhancers	Ovary	ovary
37	chr7:50855200-50856200	Enhancers	Right Ventricle	heart
38	chr7:50855200-50856400	Enhancers	Psoas Muscle	Psoas
39	chr7:50855200-50856600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:50855200-50856800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:50855200-50856800	ZNF genes & repeats	Fetal Stomach	stomach
42	chr7:50855200-50857200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:50855200-50857200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr7:50855200-50857200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:50855200-50857200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:50855200-50857200	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr7:50855200-50857200	ZNF genes & repeats	Spleen	Spleen
48	chr7:50855200-50857400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:50855200-50857400	ZNF genes & repeats	Hela-S3	cervix
50	chr7:50855200-50858000	Genic enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links