Variant report

Variant	rs17004906
Chromosome Location	chr4:81386333-81386334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:81384214..81388026-chr4:81394205..81396994,3	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10031438	0.84[CHB][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs1039054	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099227	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11099231	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11099233	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11099236	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099238	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156872	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11721676	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723594	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724838	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727411	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11729082	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11731757	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11736014	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11736601	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11929913	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11930816	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11932267	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11933863	0.85[ASN][1000 genomes]
rs11936241	0.83[ASN][1000 genomes]
rs11936436	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11936703	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11938178	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11939741	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11943326	0.81[ASN][1000 genomes]
rs11944059	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11946412	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11947437	0.85[ASN][1000 genomes]
rs12501575	0.82[EUR][1000 genomes]
rs13108814	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13129145	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1390254	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1458026	0.83[CHB][hapmap]
rs1458045	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs17004891	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17004929	0.81[ASN][1000 genomes]
rs17004930	0.81[ASN][1000 genomes]
rs17004931	0.81[ASN][1000 genomes]
rs17004932	0.82[ASN][1000 genomes]
rs1845693	0.81[ASN][1000 genomes]
rs1994981	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1994982	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2047235	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2201531	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28463662	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4370132	0.83[ASN][1000 genomes]
rs55912262	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56054570	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57025153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57650377	0.81[ASN][1000 genomes]
rs57686880	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57871169	0.83[ASN][1000 genomes]
rs60513752	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60554077	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61325136	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6534957	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6821676	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6821990	0.82[EUR][1000 genomes]
rs6842892	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72860771	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72860772	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72860777	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72860781	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72860789	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72860798	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72862015	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72874050	0.81[ASN][1000 genomes]
rs72874056	0.83[ASN][1000 genomes]
rs72874095	0.83[ASN][1000 genomes]
rs7654257	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670914	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7695356	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7699572	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9307683	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9990885	0.85[EUR][1000 genomes];0.93[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	nsv999334	chr4:81324288-81409040	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv537153	chr4:81324288-81409040	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17004906	SCD5	cis	parietal	SCAN
rs17004906	MRPS18C	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:81376200-81386400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:81381400-81389200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:81382800-81392400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:81383400-81386400	Weak transcription	HMEC	breast
5	chr4:81383400-81392000	Weak transcription	Fetal Kidney	kidney
6	chr4:81383800-81386400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:81383800-81392000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:81383800-81392800	Weak transcription	Fetal Lung	lung
9	chr4:81384000-81386400	Weak transcription	NHEK	skin
10	chr4:81384000-81391400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:81384000-81393000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:81384200-81386400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:81384200-81386600	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:81384200-81386800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:81384800-81392800	Weak transcription	Osteobl	bone
16	chr4:81385000-81386600	Weak transcription	Ovary	ovary
17	chr4:81385600-81386600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:81386200-81387000	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links