Variant report

Variant	rs6482235
Chromosome Location	chr10:23022966-23022967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:23015053..23017126-chr10:23022696..23025104,2	MCF-7	breast:
2	chr10:23022751..23025731-chr10:23344212..23345914,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1062190	1.00[JPT][hapmap]
rs10764338	1.00[JPT][hapmap]
rs11013054	0.88[JPT][hapmap]
rs11013104	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs11013110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11013113	0.87[EUR][1000 genomes]
rs1132816	0.95[ASN][1000 genomes]
rs11592427	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1171496	0.86[JPT][hapmap]
rs1171505	1.00[JPT][hapmap]
rs12259159	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12261508	1.00[JPT][hapmap]
rs1326341	1.00[JPT][hapmap]
rs16922479	1.00[JPT][hapmap]
rs1750756	0.88[JPT][hapmap]
rs1750757	1.00[JPT][hapmap]
rs1750758	0.88[JPT][hapmap]
rs1750770	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1778303	0.88[JPT][hapmap]
rs1778304	0.86[JPT][hapmap]
rs1778351	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1778356	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs1891878	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2068496	0.94[EUR][1000 genomes]
rs2364738	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2559522	0.88[JPT][hapmap]
rs2559523	0.88[JPT][hapmap]
rs2559524	0.86[JPT][hapmap]
rs2765995	0.88[JPT][hapmap]
rs2798982	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs2913109	0.88[JPT][hapmap]
rs6482229	0.88[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6482232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6482233	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482234	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6482236	0.96[EUR][1000 genomes]
rs7068999	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071450	0.88[JPT][hapmap]
rs7072589	0.93[EUR][1000 genomes]
rs7073783	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7082741	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7085322	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091585	0.94[EUR][1000 genomes]
rs7091875	0.94[EUR][1000 genomes]
rs7092404	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7094187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095326	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7097599	0.99[EUR][1000 genomes]
rs7098460	0.88[JPT][hapmap]
rs7100792	0.99[EUR][1000 genomes]
rs71491932	0.82[EUR][1000 genomes]
rs7894778	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7897908	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7912144	0.88[JPT][hapmap]
rs7915600	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7916957	1.00[JPT][hapmap]
rs7923171	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831809	chr10:22918101-23069676	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv550210	chr10:23012096-23064702	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv550211	chr10:23020350-23079385	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6482235	PIP4K2A	cis	Lymphoblastoid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:23016400-23027600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr10:23020000-23029800	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links