Variant report

Variant	rs6889653
Chromosome Location	chr5:43426309-43426310
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43411868..43414040-chr5:43425825..43427367,2	MCF-7	breast:
2	chr5:43425054..43426956-chr5:43427045..43428546,2	MCF-7	breast:
3	chr5:43425434..43428168-chr5:43429895..43432918,3	K562	blood:
4	chr5:43420922..43425218-chr5:43425765..43430067,4	MCF-7	breast:
5	chr5:43420341..43428921-chr5:43480819..43486060,17	MCF-7	breast:
6	chr5:43424455..43437851-chr5:43481449..43486495,21	MCF-7	breast:
7	chr5:43425564..43427749-chr5:43427854..43431267,3	MCF-7	breast:
8	chr5:43311545..43313404-chr5:43425545..43427890,2	MCF-7	breast:
9	chr5:43290292..43291881-chr5:43423883..43426499,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000151882	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000112972	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10058080	1.00[JPT][hapmap]
rs10066349	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10069318	0.85[ASN][1000 genomes]
rs1025299	1.00[JPT][hapmap]
rs10461740	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10461741	1.00[JPT][hapmap]
rs10941642	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs12656248	0.87[ASN][1000 genomes]
rs12656650	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12657635	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12657724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12659627	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13154319	1.00[CEU][hapmap]
rs13155622	1.00[CEU][hapmap]
rs13155888	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13159247	0.89[ASN][1000 genomes]
rs13160431	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13161149	1.00[JPT][hapmap]
rs13165869	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13167785	0.89[ASN][1000 genomes]
rs13167838	1.00[CEU][hapmap]
rs13167974	0.89[ASN][1000 genomes]
rs13168053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13169908	1.00[CEU][hapmap]
rs13173517	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13177107	1.00[JPT][hapmap]
rs13180902	1.00[CEU][hapmap]
rs13186439	1.00[CEU][hapmap]
rs13190188	0.89[ASN][1000 genomes]
rs13356232	1.00[JPT][hapmap]
rs16873315	0.88[AFR][1000 genomes]
rs16873319	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16873404	1.00[JPT][hapmap]
rs2042950	1.00[JPT][hapmap]
rs34057521	0.89[ASN][1000 genomes]
rs34087297	0.87[ASN][1000 genomes]
rs34181466	0.89[ASN][1000 genomes]
rs34353246	0.82[ASN][1000 genomes]
rs34388270	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34685576	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35141306	0.89[ASN][1000 genomes]
rs35929451	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3733767	1.00[JPT][hapmap]
rs3756417	1.00[JPT][hapmap]
rs3792917	1.00[JPT][hapmap]
rs3806871	1.00[CEU][hapmap]
rs3822423	1.00[JPT][hapmap]
rs4264950	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4438885	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4498257	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4529199	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4533897	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4554231	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56729517	0.86[AFR][1000 genomes]
rs6862588	1.00[JPT][hapmap]
rs6867927	0.85[YRI][hapmap]
rs6886399	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs6890108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6890419	0.90[YRI][hapmap]
rs6892337	1.00[JPT][hapmap]
rs6896527	0.90[YRI][hapmap]
rs6897816	0.82[YRI][hapmap]
rs71629168	0.89[ASN][1000 genomes]
rs71629169	0.87[ASN][1000 genomes]
rs7713529	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7720858	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7728139	0.82[YRI][hapmap]
rs7731345	0.86[AFR][1000 genomes]
rs7736173	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7736174	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7737947	1.00[JPT][hapmap]
rs9292877	1.00[JPT][hapmap]

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43419000-43432600	Weak transcription	Colonic Mucosa	Colon
2	chr5:43420600-43430200	Weak transcription	Gastric	stomach
3	chr5:43422000-43432600	Weak transcription	Pancreas	Pancrea
4	chr5:43422800-43428400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:43422800-43432800	Weak transcription	NH-A	brain
6	chr5:43423000-43428200	Weak transcription	Liver	Liver
7	chr5:43425000-43426400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:43425400-43426800	Enhancers	HSMMtube	muscle
9	chr5:43425400-43427400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:43425400-43427800	Enhancers	Hela-S3	cervix
11	chr5:43425600-43426400	Enhancers	Stomach Mucosa	stomach
12	chr5:43425600-43426600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:43425600-43426800	Enhancers	Osteobl	bone
14	chr5:43425600-43427800	Enhancers	A549	lung
15	chr5:43425600-43430400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:43425800-43426400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:43425800-43426600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:43425800-43426600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:43425800-43426600	Enhancers	HSMM	muscle
20	chr5:43425800-43426800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr5:43425800-43430400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:43425800-43430400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:43425800-43430400	Enhancers	HMEC	breast
24	chr5:43425800-43430400	Enhancers	NHEK	skin
25	chr5:43426000-43426400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:43426200-43426400	Enhancers	Esophagus	oesophagus
27	chr5:43426200-43426400	Enhancers	NHDF-Ad	bronchial
28	chr5:43426200-43426600	Enhancers	NHLF	lung
29	chr5:43426200-43426800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links