Variant report

Variant	rs6023156
Chromosome Location	chr20:52979515-52979516
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57921876..57923469-chr20:52978562..52980794,2	MCF-7	breast:
2	chr20:52886227..52888754-chr20:52977596..52979522,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1321464	0.81[JPT][hapmap]
rs1321465	0.81[JPT][hapmap]
rs1321468	0.81[JPT][hapmap]
rs1358806	0.82[ASN][1000 genomes]
rs1358807	0.82[ASN][1000 genomes]
rs1407043	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1590206	0.81[ASN][1000 genomes]
rs16999559	0.92[GIH][hapmap]
rs16999597	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1841860	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923118	0.90[ASN][1000 genomes]
rs2126676	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28406117	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28429972	0.96[ASN][1000 genomes]
rs2870329	0.82[ASN][1000 genomes]
rs56881371	0.99[ASN][1000 genomes]
rs59924072	0.96[ASN][1000 genomes]
rs6013987	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6013989	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs6013997	0.82[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6013999	0.90[ASN][1000 genomes]
rs6014003	0.90[ASN][1000 genomes]
rs6014004	0.88[ASN][1000 genomes]
rs6014005	0.89[ASN][1000 genomes]
rs6023153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023154	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6023155	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023158	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs6023163	0.96[ASN][1000 genomes]
rs6023164	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023178	0.81[ASN][1000 genomes]
rs6023179	0.81[ASN][1000 genomes]
rs6023180	0.92[ASN][1000 genomes]
rs6023181	0.81[ASN][1000 genomes]
rs6023183	0.83[ASN][1000 genomes]
rs6023185	0.88[ASN][1000 genomes]
rs6023189	0.90[ASN][1000 genomes]
rs6023192	0.89[ASN][1000 genomes]
rs6023193	0.89[ASN][1000 genomes]
rs6023197	0.82[ASN][1000 genomes]
rs6023203	0.90[ASN][1000 genomes]
rs6091856	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6097934	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6097938	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6097939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097940	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097941	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6097945	0.93[ASN][1000 genomes]
rs6097946	0.93[ASN][1000 genomes]
rs6097955	0.81[ASN][1000 genomes]
rs6097957	0.82[ASN][1000 genomes]
rs6097963	0.82[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs6097964	0.81[ASN][1000 genomes]
rs6097967	0.81[ASN][1000 genomes]
rs73624107	0.94[ASN][1000 genomes]
rs73624108	0.96[ASN][1000 genomes]
rs73624110	0.96[ASN][1000 genomes]
rs793033	0.81[EUR][1000 genomes];0.87[ASN][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	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	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
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6023156	ATP9A	cis	parietal	SCAN
rs6023156	ZNF217	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52976600-52983400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:52976600-52985200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr20:52977600-52985200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr20:52977800-52985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:52978200-52979600	Enhancers	Ovary	ovary
6	chr20:52978800-52979800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:52979200-52984800	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links