Variant report

Variant	rs6023096
Chromosome Location	chr20:52914728-52914729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52908114..52910241-chr20:52912363..52914987,2	MCF-7	breast:
2	chr20:52902572..52903442-chr20:52914717..52915419,2	MCF-7	breast:
3	chr20:52912716..52914955-chr20:53070123..53071877,2	MCF-7	breast:
4	chr20:52824392..52826194-chr20:52913141..52916044,3	MCF-7	breast:
5	chr20:52911450..52915662-chr20:52921093..52925920,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

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

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

rs_ID	r²[population]
rs1040857	0.93[ASN][1000 genomes]
rs10485791	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs1157418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1293134	0.93[ASN][1000 genomes]
rs1343081	0.93[ASN][1000 genomes]
rs1477734	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1477735	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs16999299	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs16999320	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16999351	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]
rs16999389	0.82[ASN][1000 genomes]
rs16999393	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs28372633	0.89[ASN][1000 genomes]
rs28460139	0.90[ASN][1000 genomes]
rs292116	0.85[CEU][hapmap]
rs292142	0.81[ASN][1000 genomes]
rs56947353	0.82[ASN][1000 genomes]
rs6013948	0.93[ASN][1000 genomes]
rs6013954	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6013957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013964	0.88[ASN][1000 genomes]
rs6023079	1.00[CEU][hapmap]
rs6023086	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6023089	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.97[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6023092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6023105	0.94[ASN][1000 genomes]
rs6023107	0.88[ASN][1000 genomes]
rs60650892	0.82[ASN][1000 genomes]
rs60900910	0.82[ASN][1000 genomes]
rs6097910	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs6097911	0.82[ASN][1000 genomes]
rs6097912	0.82[ASN][1000 genomes]
rs67043187	0.82[ASN][1000 genomes]
rs67291713	0.82[ASN][1000 genomes]
rs67348261	0.82[ASN][1000 genomes]
rs67738640	0.82[ASN][1000 genomes]
rs7265344	0.82[ASN][1000 genomes]
rs7266330	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs768113	0.82[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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52910000-52915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:52911400-52915000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links