Variant report

Variant	rs11983539
Chromosome Location	chr7:50863651-50863652
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr7:50863560-50863710	AG10803	skin:	n/a	n/a
2	CTCF	chr7:50863510-50863711	MCF-7	breast:	n/a	n/a
3	CTCF	chr7:50863560-50863710	HRPEpiC	eye:	n/a	n/a
4	CTCF	chr7:50863528-50863683	ProgFib	skin:	n/a	n/a
5	CTCF	chr7:50863560-50863710	HEEpiC	esophagus:	n/a	n/a
6	CTCF	chr7:50863376-50863766	HCT-116	colon:	n/a	n/a
7	CTCF	chr7:50863492-50863734	MCF-7	breast:	n/a	n/a
8	CTCF	chr7:50863540-50863690	HPAF	blood vessel:	n/a	n/a
9	RAD21	chr7:50863499-50863782	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr7:50863367-50863894	A549	lung:	n/a	n/a
11	CTCF	chr7:50863560-50863710	Caco-2	colon:	n/a	n/a
12	CTCF	chr7:50863540-50863690	HRE	kidney:	n/a	n/a
13	CTCF	chr7:50863514-50863705	LNCaP	prostate:	n/a	n/a
14	CTCF	chr7:50863526-50863681	LNCaP	prostate:	n/a	n/a
15	CTCF	chr7:50863560-50863710	HAc	cerebellar:	n/a	n/a
16	CTCF	chr7:50863560-50863710	HUVEC	blood vessel:	n/a	n/a
17	CTCF	chr7:50863492-50863731	MCF-7	breast:	n/a	n/a
18	CTCF	chr7:50863560-50863710	HepG2	liver:	n/a	n/a
19	CTCF	chr7:50863413-50863776	T-47D	breast:	n/a	n/a
20	RAD21	chr7:50863351-50863799	A549	lung:	n/a	n/a
21	CTCF	chr7:50863488-50863776	A549	lung:	n/a	n/a
22	CTCF	chr7:50863279-50864021	A549	lung:	n/a	n/a
23	CTCF	chr7:50863560-50863710	SAEC	small airway:	n/a	n/a
24	RAD21	chr7:50863513-50863752	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr7:50863540-50863690	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr7:50863484-50863761	MCF-7	breast:	n/a	n/a
27	RAD21	chr7:50863464-50863736	HepG2	liver:	n/a	n/a
28	CTCF	chr7:50863540-50863690	HA-sp	spinal cord:	n/a	n/a
29	CTCF	chr7:50863540-50863690	HBMEC	blood vessel:	n/a	n/a
30	RAD21	chr7:50863501-50863690	HepG2	liver:	n/a	n/a
31	CTCF	chr7:50863580-50863730	HVMF	connective:	n/a	n/a
32	CTCF	chr7:50863520-50863670	HMEC	breast:	n/a	n/a
33	CTCF	chr7:50863520-50863670	AG04449	skin:	n/a	n/a
34	CTCF	chr7:50863600-50863750	NHEK	skin:	n/a	n/a
35	MAX	chr7:50863629-50863947	Hela-S3	cervix:	n/a	chr7:50863861-50863871 chr7:50863875-50863885
36	CTCF	chr7:50863520-50863670	NB4	blood:	n/a	n/a
37	CTCF	chr7:50863520-50863670	HPAF	blood vessel:	n/a	n/a
38	CTCF	chr7:50863520-50863670	HRPEpiC	eye:	n/a	n/a
39	CTCF	chr7:50863552-50863672	Medullo	brain:	n/a	n/a
40	CTCF	chr7:50863520-50863670	NHDF-neo	bronchial:	n/a	n/a
41	CTCF	chr7:50863540-50863690	HCFaa	heart:	n/a	n/a
42	RAD21	chr7:50863360-50863918	MCF-7	breast:	n/a	n/a
43	RAD21	chr7:50863431-50863812	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr7:50863560-50863710	HCPEpiC	choroid plexus:	n/a	n/a
45	RAD21	chr7:50863541-50863742	A549	lung:	n/a	n/a
46	CTCF	chr7:50863520-50863670	BJ	skin:	n/a	n/a
47	CTCF	chr7:50863520-50863690	A549	lung:	n/a	n/a
48	CTCF	chr7:50863506-50863750	K562	blood:	n/a	n/a
49	RAD21	chr7:50863300-50863940	HCT-116	colon:	n/a	n/a
50	CTCF	chr7:50863495-50863669	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50863097..50863770-chr7:51135545..51136174,2	MCF-7	breast:
2	chr7:50826033..50828575-chr7:50862954..50865716,2	K562	blood:

No data

Variant related genes	Relation type
GRB10	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

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];0.93[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[AFR][1000 genomes];0.91[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];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs10226937	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10231012	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10235345	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10239268	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1024531	0.84[AMR][1000 genomes]
rs10248029	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10258458	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10264904	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10268643	0.88[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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10276986	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10278363	0.83[CEU][hapmap]
rs10281065	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10464765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464790	1.00[AFR][1000 genomes];1.00[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];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238310	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238311	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238313	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238315	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11238325	0.90[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];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.99[AFR][1000 genomes];0.98[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];0.93[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];1.00[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];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763072	0.85[JPT][hapmap]
rs11974751	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11978750	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665949	0.93[CEU][hapmap]
rs12671577	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12674028	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718927	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12718930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232029	0.85[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051895	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2051896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074719	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074720	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2074721	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074722	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074777	0.85[JPT][hapmap]
rs2158670	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286152	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2286154	0.93[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2329554	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876846	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801000	0.84[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];0.96[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6593173	0.85[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];0.91[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6593180	1.00[AFR][1000 genomes];0.98[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];0.85[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945597	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6946194	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6951356	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6957007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6958750	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6960912	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6963498	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]
rs6966774	0.88[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];0.85[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.94[AFR][1000 genomes];0.98[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];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs734422	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs757773	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[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];0.87[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs757777	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs757778	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785908	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7785914	0.85[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];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7788511	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791286	0.91[GIH][hapmap];0.81[AFR][1000 genomes]
rs7793570	0.84[JPT][hapmap]
rs7802338	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803278	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs886700	0.88[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
rs11983539	VWC2	cis	cerebellum	SCAN
rs11983539	LOC100129427	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50861000-50867400	Weak transcription	Spleen	Spleen
2	chr7:50861800-50864200	Enhancers	K562	blood
3	chr7:50861800-50867600	Weak transcription	Psoas Muscle	Psoas
4	chr7:50862200-50867400	Weak transcription	Left Ventricle	heart
5	chr7:50862200-50889000	Weak transcription	Right Atrium	heart
6	chr7:50863000-50864000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:50863200-50864000	Enhancers	A549	lung
8	chr7:50863200-50865000	Enhancers	Pancreas	Pancrea

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