Variant report

Variant	rs11962730
Chromosome Location	chr6:140063979-140063980
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140062822..140064897-chr6:140067790..140070616,2	K562	blood:
2	chr6:140059888..140061775-chr6:140062936..140065561,3	MCF-7	breast:
3	chr6:139695200..139697072-chr6:140062623..140064203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10499213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499214	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11963532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964275	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12055436	0.80[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12055472	0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12055843	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12662206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17069206	0.88[JPT][hapmap]
rs17069225	0.88[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.81[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1891808	0.83[AFR][1000 genomes]
rs1936210	0.89[ASN][1000 genomes]
rs1936214	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2096283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096284	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2185923	0.88[ASN][1000 genomes]
rs2327993	0.88[ASN][1000 genomes]
rs4520026	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4535566	0.86[ASN][1000 genomes]
rs55764205	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55966840	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs60350063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60758082	0.88[ASN][1000 genomes]
rs6570372	0.89[ASN][1000 genomes]
rs6570373	0.90[ASN][1000 genomes]
rs6570374	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6901783	0.94[JPT][hapmap]
rs6905478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6933318	0.94[JPT][hapmap]
rs73556090	0.88[ASN][1000 genomes]
rs73558032	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743796	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7752001	0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7752323	0.89[ASN][1000 genomes]
rs7756866	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7769567	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7774968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9321752	0.88[ASN][1000 genomes]
rs9373246	0.82[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9373247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9376452	0.80[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs9376457	0.89[ASN][1000 genomes]
rs9376466	0.81[EUR][1000 genomes]
rs9385874	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9385875	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9385876	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9389715	0.89[ASN][1000 genomes]
rs9389717	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9399292	0.88[JPT][hapmap]
rs9403113	0.88[ASN][1000 genomes]
rs9403114	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9403115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9403116	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][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	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
2	nsv464065	chr6:140027836-140085873	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv604766	chr6:140027836-140085873	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv830820	chr6:140059279-140255292	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11962730	MAP3K5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140054800-140072000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:140055000-140064600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:140060600-140065400	Weak transcription	Adipose Nuclei	Adipose
4	chr6:140060800-140064000	Weak transcription	A549	lung
5	chr6:140060800-140064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:140062800-140065800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:140063200-140064000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:140063400-140064000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr6:140063400-140064200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr6:140063400-140064200	Enhancers	Gastric	stomach
11	chr6:140063400-140064400	Enhancers	Muscle Satellite Cultured Cells	--
12	chr6:140063400-140064800	Enhancers	HSMMtube	muscle
13	chr6:140063400-140066600	Enhancers	NHDF-Ad	bronchial
14	chr6:140063600-140065400	Enhancers	HepG2	liver
15	chr6:140063600-140066200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:140063600-140067200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:140063800-140064000	Enhancers	Colon Smooth Muscle	Colon
18	chr6:140063800-140066000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:140063800-140066000	Enhancers	HSMM	muscle
20	chr6:140063800-140066400	Enhancers	NHLF	lung
21	chr6:140063800-140069000	Weak transcription	Fetal Heart	heart

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