Variant report

Variant	rs590856
Chromosome Location	chr6:139844429-139844430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:139694016..139698110-chr6:139843661..139847617,3	K562	blood:
2	chr6:139693301..139695661-chr6:139842764..139846349,4	K562	blood:
3	chr6:139843608..139846109-chr6:139850939..139853021,2	MCF-7	breast:
4	chr6:139839378..139842332-chr6:139842713..139845287,3	K562	blood:
5	chr6:139836503..139839268-chr6:139841620..139844665,3	K562	blood:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11155073	0.80[EUR][1000 genomes]
rs17585887	0.81[EUR][1000 genomes]
rs17585915	0.81[EUR][1000 genomes]
rs4896469	0.89[CHB][hapmap];0.87[ASN][1000 genomes]
rs589235	0.85[EUR][1000 genomes]
rs592423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs605066	0.80[EUR][1000 genomes]
rs607342	0.80[EUR][1000 genomes]
rs608736	0.85[EUR][1000 genomes]
rs628751	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[EUR][1000 genomes]
rs634869	0.80[EUR][1000 genomes]
rs635243	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs636202	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643381	0.84[EUR][1000 genomes]
rs651837	0.80[EUR][1000 genomes]
rs654689	0.81[EUR][1000 genomes]
rs668459	0.81[EUR][1000 genomes]
rs672457	0.81[EUR][1000 genomes]
rs6916642	0.84[YRI][hapmap]
rs9800462	0.89[CHB][hapmap];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Red blood cell traits	23222517	GWAS catalog

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:139832000-139855200	Weak transcription	Right Atrium	heart
2	chr6:139840400-139844800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:139840800-139855200	Weak transcription	Pancreas	Pancrea
4	chr6:139841000-139844800	Enhancers	HMEC	breast
5	chr6:139841000-139854600	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:139841600-139849400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr6:139841600-139853000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:139842000-139846200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:139842600-139854800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:139842600-139861200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:139843800-139846400	Weak transcription	Placenta	Placenta
12	chr6:139844000-139845800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:139844200-139845200	Weak transcription	Hela-S3	cervix
14	chr6:139844200-139846600	Weak transcription	Fetal Heart	heart
15	chr6:139844400-139845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:139844400-139846000	Weak transcription	NHDF-Ad	bronchial
17	chr6:139844400-139846200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:139844400-139846600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:139844400-139846600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:139844400-139847000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:139844400-139851800	Weak transcription	Fetal Lung	lung

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