Variant report

Variant	rs6890108
Chromosome Location	chr5:43426467-43426468
allele	C/T
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
ENSG00000112972	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000151882	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10058080	1.00[JPT][hapmap]
rs10066349	0.87[ASN][1000 genomes]
rs10069318	0.83[ASN][1000 genomes]
rs1025299	1.00[JPT][hapmap]
rs10461740	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10461741	1.00[JPT][hapmap]
rs10941642	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap]
rs12656248	0.89[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[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13154319	1.00[CEU][hapmap]
rs13155622	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs13155888	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13159247	0.87[ASN][1000 genomes]
rs13160431	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs13161149	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs13165869	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13167785	0.87[ASN][1000 genomes]
rs13167838	1.00[CEU][hapmap]
rs13167974	0.87[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	0.87[ASN][1000 genomes]
rs13356232	1.00[JPT][hapmap]
rs16873319	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs16873327	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs16873404	1.00[JPT][hapmap]
rs2042950	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs34057521	0.87[ASN][1000 genomes]
rs34087297	0.89[ASN][1000 genomes]
rs34181466	0.87[ASN][1000 genomes]
rs34353246	0.84[ASN][1000 genomes]
rs34388270	0.87[ASN][1000 genomes]
rs34685576	0.87[ASN][1000 genomes]
rs35141306	0.87[ASN][1000 genomes]
rs35929451	0.87[ASN][1000 genomes]
rs3733767	1.00[JPT][hapmap]
rs3756417	1.00[JPT][hapmap]
rs3792917	1.00[JPT][hapmap]
rs3806871	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs3822423	1.00[JPT][hapmap]
rs4264950	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs4438885	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4498257	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4529199	0.85[ASN][1000 genomes]
rs4533897	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4554231	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6451689	0.85[AFR][1000 genomes]
rs6451690	0.85[AFR][1000 genomes]
rs6862588	1.00[JPT][hapmap]
rs6881601	0.82[ASW][hapmap]
rs6881870	0.85[AFR][1000 genomes]
rs6889653	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6892337	1.00[JPT][hapmap]
rs71629168	0.87[ASN][1000 genomes]
rs71629169	0.89[ASN][1000 genomes]
rs7712723	0.85[YRI][hapmap]
rs7713529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7716564	0.93[YRI][hapmap]
rs7720858	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs7736173	0.87[ASN][1000 genomes]
rs7736174	0.87[ASN][1000 genomes]
rs7737947	1.00[JPT][hapmap]
rs9292877	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9687416	0.85[AFR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6890108	Hs.482037	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 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	chr5:43425400-43426800	Enhancers	HSMMtube	muscle
8	chr5:43425400-43427400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:43425400-43427800	Enhancers	Hela-S3	cervix
10	chr5:43425600-43426600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:43425600-43426800	Enhancers	Osteobl	bone
12	chr5:43425600-43427800	Enhancers	A549	lung
13	chr5:43425600-43430400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:43425800-43426600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:43425800-43426600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:43425800-43426600	Enhancers	HSMM	muscle
17	chr5:43425800-43426800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr5:43425800-43430400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:43425800-43430400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:43425800-43430400	Enhancers	HMEC	breast
21	chr5:43425800-43430400	Enhancers	NHEK	skin
22	chr5:43426200-43426600	Enhancers	NHLF	lung
23	chr5:43426200-43426800	Enhancers	HepG2	liver
24	chr5:43426400-43427000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:43426400-43427800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:43426400-43429200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:43426400-43443600	Weak transcription	Esophagus	oesophagus

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