Variant report

Variant	rs10516738
Chromosome Location	chr4:81954086-81954087
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:81953825..81956176-chr4:81958029..81960138,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10005851	0.92[JPT][hapmap]
rs10007784	0.92[JPT][hapmap]
rs10019046	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11099459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642476	0.92[JPT][hapmap]
rs13122304	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133972	0.82[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138361	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13141362	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495634	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495637	0.91[JPT][hapmap]
rs17005034	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903746	0.92[JPT][hapmap]
rs34042179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094604	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3733549	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4389567	0.92[JPT][hapmap]
rs6831641	1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71596047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659948	0.96[EUR][1000 genomes]
rs7661611	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7697151	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924048	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985328	0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1006466	chr4:81888983-82009675	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:81951000-81954800	Active TSS	Duodenum Mucosa	Duodenum
2	chr4:81951200-81954200	Active TSS	Ovary	ovary
3	chr4:81951200-81955400	Active TSS	Rectal Smooth Muscle	rectum
4	chr4:81951800-81954200	Bivalent/Poised TSS	Fetal Lung	lung
5	chr4:81953200-81954800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr4:81953200-81955200	Bivalent/Poised TSS	Fetal Brain Female	brain
7	chr4:81953200-81955400	Active TSS	Fetal Stomach	stomach
8	chr4:81953200-81956200	Active TSS	Stomach Smooth Muscle	stomach
9	chr4:81953400-81954800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:81953400-81954800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr4:81953400-81955400	Active TSS	Brain Germinal Matrix	brain
12	chr4:81953600-81954200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr4:81953600-81954800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
14	chr4:81953600-81955000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
15	chr4:81953600-81955000	Active TSS	Primary B cells from cord blood	blood
16	chr4:81953600-81955400	Active TSS	Colon Smooth Muscle	Colon
17	chr4:81953800-81954200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr4:81953800-81954200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:81954000-81954200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
20	chr4:81954000-81954200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:81954000-81954200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr4:81954000-81955000	Weak transcription	Fetal Intestine Small	intestine

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