Variant report

Variant	rs6943153
Chromosome Location	chr7:50791579-50791580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50790225..50792991-chr7:50795647..50797748,2	K562	blood:
2	chr7:50790685..50792976-chr7:50798352..50800555,2	MCF-7	breast:
3	chr7:50787237..50792773-chr7:50859512..50862102,5	K562	blood:
4	chr7:50790851..50793423-chr7:50808452..50810268,2	K562	blood:

Variant related genes	Relation type
ENSG00000106070	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1014384	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs1019000	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10226937	0.82[AMR][1000 genomes]
rs1024529	0.81[AFR][1000 genomes]
rs1024531	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10248029	0.82[AMR][1000 genomes]
rs10258458	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10264904	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10265504	0.84[ASN][1000 genomes]
rs10268643	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10281065	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10486761	0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11238297	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11238310	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11238311	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11238313	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11238315	0.87[AMR][1000 genomes]
rs11238326	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs11238337	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs11763072	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11763778	0.97[ASN][1000 genomes]
rs11765762	0.97[ASN][1000 genomes]
rs11974751	0.82[AMR][1000 genomes]
rs11983539	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs12536500	0.83[LWK][hapmap];0.83[YRI][hapmap]
rs12668316	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13232029	0.83[AMR][1000 genomes]
rs13311390	0.84[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1962391	0.92[AFR][1000 genomes]
rs2058014	0.92[ASN][1000 genomes]
rs2074719	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2074720	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2074721	0.87[AMR][1000 genomes]
rs2074722	0.87[AMR][1000 genomes]
rs2074777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2108349	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2190502	0.92[ASN][1000 genomes]
rs2214963	0.92[ASN][1000 genomes]
rs2237490	0.86[ASN][1000 genomes]
rs2286152	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2286154	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2299153	0.92[ASN][1000 genomes]
rs2329489	0.92[ASN][1000 genomes]
rs2876846	0.88[AMR][1000 genomes]
rs3801000	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4521715	0.93[CHB][hapmap];0.92[ASN][1000 genomes]
rs4947806	0.97[ASN][1000 genomes]
rs6593164	0.87[CHD][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6593173	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6593174	0.85[CHD][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs6943901	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6945597	0.88[AMR][1000 genomes]
rs6946194	0.86[AMR][1000 genomes]
rs6951356	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6960912	0.85[AMR][1000 genomes]
rs6963498	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6966774	0.88[AMR][1000 genomes]
rs6967612	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971834	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs6979369	0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs734422	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs757773	0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs757774	0.87[CHD][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7782797	0.82[YRI][hapmap];0.93[AFR][1000 genomes]
rs7785908	0.87[AMR][1000 genomes]
rs7785914	0.87[AMR][1000 genomes]
rs7786917	0.85[JPT][hapmap]
rs7793570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7809623	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7809775	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs886700	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs933360	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1031138	chr7:50651793-50814881	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6943153	VWC2	cis	cerebellum	SCAN
rs6943153	LOC100129427	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50742600-50792000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:50763400-50806800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:50772000-50791600	Weak transcription	K562	blood
4	chr7:50773000-50807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:50777600-50792600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr7:50780600-50795000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:50780600-50807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:50780800-50801400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr7:50781000-50794800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:50781200-50795600	Weak transcription	NHDF-Ad	bronchial
11	chr7:50781200-50797600	Weak transcription	HSMMtube	muscle
12	chr7:50781200-50798200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:50783000-50792000	Weak transcription	HSMM	muscle
14	chr7:50783800-50798200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:50783800-50798400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:50784000-50799400	Weak transcription	Hela-S3	cervix
17	chr7:50786800-50795400	Weak transcription	Fetal Kidney	kidney
18	chr7:50787000-50792600	Weak transcription	Osteobl	bone
19	chr7:50787000-50797800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:50787000-50797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:50787000-50798600	Weak transcription	Brain Germinal Matrix	brain
22	chr7:50787000-50807600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:50787800-50794800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr7:50787800-50798200	Weak transcription	HepG2	liver
25	chr7:50788000-50816000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:50788200-50796200	Weak transcription	Small Intestine	intestine
27	chr7:50788800-50792200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr7:50789200-50793000	Enhancers	Spleen	Spleen
29	chr7:50789400-50798600	Weak transcription	A549	lung
30	chr7:50789400-50811600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:50789600-50791600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:50789600-50793200	Enhancers	Primary hematopoietic stem cells	blood
33	chr7:50789600-50794600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr7:50789600-50798200	Weak transcription	Brain Anterior Caudate	brain
35	chr7:50789600-50798400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr7:50789600-50807400	Weak transcription	Esophagus	oesophagus
37	chr7:50789800-50791600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:50789800-50791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:50789800-50792200	Weak transcription	NH-A	brain
40	chr7:50789800-50794600	Weak transcription	Colon Smooth Muscle	Colon
41	chr7:50789800-50795000	Weak transcription	NHLF	lung
42	chr7:50789800-50797400	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:50789800-50797600	Weak transcription	Fetal Brain Female	brain
44	chr7:50789800-50798600	Weak transcription	Brain Angular Gyrus	brain
45	chr7:50790000-50792600	Weak transcription	Ovary	ovary
46	chr7:50790000-50794600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:50790000-50797400	Weak transcription	Brain Substantia Nigra	brain
48	chr7:50790000-50801200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr7:50790200-50791600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:50790200-50791600	Weak transcription	Gastric	stomach

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