Variant report

Variant	rs1330017
Chromosome Location	chr20:53090283-53090284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53073108..53074852-chr20:53089210..53091091,3	MCF-7	breast:
2	chr20:53068334..53071090-chr20:53089202..53090759,2	MCF-7	breast:
3	chr20:53066844..53069030-chr20:53089773..53091908,2	MCF-7	breast:
4	chr1:144917532..144918295-chr20:53090253..53091159,2	MCF-7	breast:
5	chr20:52823193..52825695-chr20:53088951..53090894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11907464	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12329481	0.88[CEU][hapmap]
rs13040866	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13042185	1.00[CEU][hapmap]
rs13042986	1.00[CEU][hapmap]
rs13044898	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16999643	0.88[CEU][hapmap]
rs34310366	0.82[EUR][1000 genomes]
rs34433522	0.81[EUR][1000 genomes]
rs34502501	0.82[EUR][1000 genomes]
rs34616206	0.83[EUR][1000 genomes]
rs34683517	0.82[EUR][1000 genomes]
rs35276316	0.82[EUR][1000 genomes]
rs6014019	0.88[CEU][hapmap]
rs6014020	0.88[CEU][hapmap]
rs6014026	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6014027	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6014032	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023244	0.88[CEU][hapmap]
rs6023245	0.88[CEU][hapmap]
rs6023251	0.88[CEU][hapmap]
rs6023254	0.88[CEU][hapmap]
rs6023262	1.00[ASN][1000 genomes]
rs6023263	1.00[ASN][1000 genomes]
rs6023265	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023266	1.00[ASN][1000 genomes]
rs6023267	1.00[ASN][1000 genomes]
rs6023268	1.00[ASN][1000 genomes]
rs6023269	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023270	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023272	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023273	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6023274	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023275	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023276	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023291	1.00[CEU][hapmap]
rs6023307	1.00[CEU][hapmap]
rs6023309	1.00[CEU][hapmap]
rs6091886	0.88[CEU][hapmap]
rs6091887	1.00[ASN][1000 genomes]
rs6091890	0.93[EUR][1000 genomes]
rs6091891	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6098003	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6098005	0.98[EUR][1000 genomes]
rs6098006	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6098007	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6098008	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6098009	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6098011	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs67687183	0.82[EUR][1000 genomes]
rs922398	1.00[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1330017	ZNF217	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53084800-53091800	Weak transcription	Aorta	Aorta
2	chr20:53088000-53091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:53088000-53091600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links