Variant report

Variant	rs6784598
Chromosome Location	chr3:119533256-119533257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119531732..119533815-chr3:119534255..119536418,2	MCF-7	breast:
2	chr3:119532575..119535119-chr3:119538231..119540719,2	K562	blood:
3	chr3:119532575..119536291-chr3:119538231..119540719,3	K562	blood:
4	chr3:119531331..119533784-chr3:119534969..119537956,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10433404	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10934500	0.91[JPT][hapmap]
rs10934502	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10934503	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11915717	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs11917714	0.87[JPT][hapmap]
rs12629015	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12634476	0.91[JPT][hapmap]
rs12634889	0.91[JPT][hapmap]
rs12638973	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs13321783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546753	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574154	0.91[JPT][hapmap]
rs1719890	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1719891	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1719894	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1732168	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1732170	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2276707	0.87[JPT][hapmap]
rs2319398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2319399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2472682	0.91[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28536662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2873950	0.86[JPT][hapmap]
rs3107669	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732358	0.82[YRI][hapmap]
rs3732359	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3732360	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs3732361	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814057	0.91[JPT][hapmap]
rs3814058	0.90[JPT][hapmap]
rs4261913	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4340737	0.91[JPT][hapmap]
rs4491945	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4624596	0.91[JPT][hapmap]
rs4688042	0.91[JPT][hapmap]
rs4688046	0.91[JPT][hapmap]
rs4688047	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs57695730	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58605236	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6438552	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6438553	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6785049	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6795653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6800622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6805251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808874	0.91[JPT][hapmap]
rs6808975	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7431209	0.86[JPT][hapmap]
rs7611736	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7620750	0.82[CEU][hapmap]
rs7633279	0.91[JPT][hapmap]
rs7639388	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs7641045	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7644234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9813864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9866394	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9873477	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9878473	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9879295	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[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	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6784598	GSK3B	cis	parietal	SCAN
rs6784598	MUC13	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119516800-119534600	Weak transcription	HepG2	liver
2	chr3:119528200-119533800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:119529400-119533600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119529400-119533600	Weak transcription	Colonic Mucosa	Colon
5	chr3:119529400-119535800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:119529400-119537000	Strong transcription	Fetal Intestine Large	intestine
7	chr3:119529400-119537800	Strong transcription	Fetal Intestine Small	intestine
8	chr3:119529400-119544000	Weak transcription	Right Atrium	heart
9	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:119529600-119536000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:119529600-119543400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
13	chr3:119529800-119543600	Weak transcription	GM12878-XiMat	blood
14	chr3:119530200-119542800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:119531400-119534600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:119531600-119536200	Weak transcription	Fetal Heart	heart
17	chr3:119532000-119543800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:119532200-119533600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:119532400-119535800	Weak transcription	Left Ventricle	heart
20	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart
21	chr3:119533200-119534400	Genic enhancers	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links