Variant report

Variant	rs62431062
Chromosome Location	chr6:140380058-140380059
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:140375571..140378188-chr6:140378713..140381591,2	K562	blood:
2	chr6:139692809..139695953-chr6:140377824..140381210,3	MCF-7	breast:
3	chr6:140362168..140365003-chr6:140377211..140380163,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164442	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10499216	0.97[ASN][1000 genomes]
rs10499219	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1113096	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11966793	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11967431	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11969633	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12523886	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12525793	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12526277	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12528420	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12529701	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12529920	0.86[EUR][1000 genomes]
rs1390500	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496114	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17069706	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17069710	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17069727	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17069741	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17069805	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17069893	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1879097	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2050716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2328026	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57789174	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59447713	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60747543	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62429521	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62429525	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62431064	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62431065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62431066	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62431098	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431099	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431110	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431142	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6915764	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs732015	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73571530	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7770431	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[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	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140373600-140381000	Weak transcription	HSMM	muscle
2	chr6:140373600-140384200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:140374200-140383800	Weak transcription	Fetal Brain Female	brain
4	chr6:140374800-140381400	Weak transcription	NHEK	skin
5	chr6:140374800-140382400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:140375000-140380200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:140375000-140381400	Weak transcription	NH-A	brain
8	chr6:140375000-140383800	Weak transcription	Brain Germinal Matrix	brain
9	chr6:140375400-140380400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:140377400-140381200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:140378000-140383000	Weak transcription	Psoas Muscle	Psoas
12	chr6:140379400-140383600	Enhancers	Hela-S3	cervix
13	chr6:140379800-140380600	Weak transcription	Placenta	Placenta
14	chr6:140379800-140385200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:140380000-140380600	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:140380000-140385200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:140380000-140385800	Enhancers	NHDF-Ad	bronchial

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