Variant report

Variant	rs2490034
Chromosome Location	chr6:3870889-3870890
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	chr6:3867578..3871255-chr6:3875568..3878363,3	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10447476	0.94[EUR][1000 genomes]
rs11242887	0.87[EUR][1000 genomes]
rs11242889	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11755819	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2490050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490052	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490053	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490054	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2490055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2496386	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9392531	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1024414	chr6:3862744-3898734	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:3867200-3871400	Enhancers	Stomach Mucosa	stomach
2	chr6:3867600-3871200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:3868000-3871200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:3868200-3871000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:3868200-3871200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:3868200-3873000	Enhancers	Liver	Liver
7	chr6:3868400-3871200	Enhancers	Placenta	Placenta
8	chr6:3868600-3872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:3868600-3876200	Weak transcription	Right Atrium	heart
10	chr6:3868800-3872400	Weak transcription	NHEK	skin
11	chr6:3868800-3874400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:3869000-3875800	Weak transcription	HSMM	muscle
13	chr6:3869200-3876000	Weak transcription	HSMMtube	muscle
14	chr6:3869600-3871000	Enhancers	Gastric	stomach
15	chr6:3869600-3871200	Enhancers	Pancreas	Pancrea
16	chr6:3869600-3871200	Flanking Active TSS	A549	lung
17	chr6:3869600-3871400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:3869800-3871000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr6:3869800-3872800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:3869800-3874400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:3870000-3871400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr6:3870000-3872400	Weak transcription	Lung	lung
23	chr6:3870000-3872600	Weak transcription	NHDF-Ad	bronchial
24	chr6:3870200-3871000	Flanking Active TSS	HepG2	liver
25	chr6:3870200-3872600	Weak transcription	Esophagus	oesophagus
26	chr6:3870200-3874400	Enhancers	Fetal Intestine Large	intestine
27	chr6:3870200-3874800	Enhancers	Fetal Intestine Small	intestine
28	chr6:3870200-3875800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:3870400-3871000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:3870600-3871000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr6:3870600-3871000	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:3870800-3871000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr6:3870800-3871000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:3870800-3871000	Enhancers	Stomach Smooth Muscle	stomach
35	chr6:3870800-3871200	Enhancers	Small Intestine	intestine
36	chr6:3870800-3872600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links