Variant report

Variant	rs2815090
Chromosome Location	chr6:39136818-39136819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:39135364..39137798-chr6:39146976..39150175,3	K562	blood:
2	chr6:39135484..39137595-chr6:39246692..39248573,2	MCF-7	breast:
3	chr6:39131553..39138589-chr6:39265255..39275264,18	MCF-7	breast:
4	chr6:39136014..39136929-chr6:39270618..39271594,3	MCF-7	breast:
5	chr6:39136536..39138327-chr6:39236604..39238179,2	MCF-7	breast:
6	chr1:149223489..149225465-chr6:39135790..39138241,2	MCF-7	breast:
7	chr6:39081584..39083702-chr6:39135173..39137222,2	MCF-7	breast:
8	chr6:39135502..39137739-chr6:39151644..39154156,2	MCF-7	breast:
9	chr6:39134049..39137396-chr6:39195548..39198485,4	MCF-7	breast:
10	chr6:39136404..39138068-chr6:39155410..39157710,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction
ENSG00000112167	Chromatin interaction
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1019772	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1155348	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12665144	1.00[ASW][hapmap]
rs1366322	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1366324	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1366325	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1465570	1.00[ASW][hapmap];0.83[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1544934	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1835004	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1864061	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1896681	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2162838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2268635	1.00[ASW][hapmap]
rs228819	1.00[ASW][hapmap];0.83[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2300612	1.00[ASW][hapmap]
rs2561416	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs2815056	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2815074	0.83[CEU][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2815075	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815079	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815088	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2815092	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380834	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs962311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[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	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39132200-39137000	Weak transcription	Gastric	stomach
2	chr6:39134400-39138800	Enhancers	Duodenum Mucosa	Duodenum
3	chr6:39134600-39139400	Weak transcription	Right Atrium	heart
4	chr6:39134800-39137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:39134800-39139400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:39135600-39139000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:39135600-39139000	Weak transcription	Fetal Intestine Small	intestine
8	chr6:39135600-39139400	Weak transcription	Fetal Lung	lung
9	chr6:39135800-39137000	Weak transcription	Lung	lung
10	chr6:39136200-39138600	Enhancers	Pancreas	Pancrea
11	chr6:39136400-39138200	Enhancers	Esophagus	oesophagus
12	chr6:39136400-39139400	Weak transcription	Fetal Stomach	stomach
13	chr6:39136600-39138400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:39136800-39138000	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr6:39136800-39138800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr6:39136800-39138800	Enhancers	Stomach Mucosa	stomach

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