Variant report

Variant	rs3890819
Chromosome Location	chr7:40461332-40461333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10234636	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10245007	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256791	0.93[CEU][hapmap]
rs10951634	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs11531505	0.99[ASN][1000 genomes]
rs11766930	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11772069	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs11980965	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12234460	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12531683	0.99[ASN][1000 genomes]
rs12532479	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12533531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12538229	0.96[ASN][1000 genomes]
rs12669577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12670267	0.94[ASN][1000 genomes]
rs12673516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1319467	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16880229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171680	0.93[CEU][hapmap]
rs17171683	0.84[JPT][hapmap]
rs17171686	0.84[JPT][hapmap]
rs17171693	0.84[JPT][hapmap]
rs17171694	0.84[JPT][hapmap]
rs17171696	0.84[JPT][hapmap]
rs17171703	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs17171704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17171705	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17171710	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2190261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2329772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143205	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs4379368	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4421260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4434532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4452702	0.93[CEU][hapmap];0.84[JPT][hapmap]
rs4526265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4563791	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4612243	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs4723954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs59682057	0.97[ASN][1000 genomes]
rs6462972	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs6462976	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs6945101	0.93[CEU][hapmap]
rs6965764	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs7782189	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807217	0.92[CEU][hapmap]
rs9690724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv887985	chr7:40265510-40586674	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv817404	chr7:40295934-40573605	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv949540	chr7:40321357-40528147	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv34484	chr7:40383159-40489083	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2757223	chr7:40384030-40497278	Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2759526	chr7:40384030-40497278	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv8081	chr7:40393228-40486239	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1016800	chr7:40409214-40470294	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1015701	chr7:40409214-40474936	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv830969	chr7:40422576-40582389	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv1027075	chr7:40438478-40479723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
13	nsv1026022	chr7:40440560-40479066	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
14	esv2761320	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
15	nsv1032028	chr7:40440560-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
16	nsv1032883	chr7:40440560-40489083	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1019992	chr7:40443653-40479723	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
18	nsv1017615	chr7:40445480-40570791	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40458400-40473200	Weak transcription	Aorta	Aorta
2	chr7:40459800-40467400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr7:40459800-40469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:40460000-40467400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr7:40460400-40464800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr7:40460400-40465000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr7:40460400-40465600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:40460800-40461400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:40461000-40462200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr7:40461200-40461600	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links