Variant report

Variant	rs482789
Chromosome Location	chr1:86452815-86452816
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86452263..86454852-chr1:86455069..86456770,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1072508	0.91[CHB][hapmap]
rs1072509	0.91[CHB][hapmap]
rs10873730	0.91[CEU][hapmap];0.90[CHB][hapmap]
rs10873731	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs1112327	0.86[CEU][hapmap]
rs11161693	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs11161695	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs11161696	0.91[CHB][hapmap]
rs11161697	0.91[CHB][hapmap]
rs12029238	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1564516	0.95[CHB][hapmap]
rs17411495	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs186376	0.86[CHB][hapmap]
rs1904947	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs313701	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs313702	0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap]
rs313703	0.90[CHB][hapmap]
rs313704	0.86[CHB][hapmap]
rs313705	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs313706	0.86[CHB][hapmap]
rs313707	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs313708	0.91[CHB][hapmap]
rs313709	0.85[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs313738	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs313740	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs313741	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs313742	0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs313746	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs313756	0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs313757	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs313758	0.81[CHB][hapmap]
rs313759	0.81[CHB][hapmap]
rs313763	0.90[CHB][hapmap]
rs313769	0.89[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs313770	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs313771	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs313775	0.89[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs428475	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs437257	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs4486475	0.85[CEU][hapmap]
rs481277	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486726	0.85[CEU][hapmap]
rs522075	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559247	0.85[CEU][hapmap]
rs570288	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs573444	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578615	0.85[CEU][hapmap]
rs593146	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603297	0.85[CEU][hapmap]
rs605060	0.85[CEU][hapmap]
rs6576793	0.86[CHB][hapmap]
rs6673508	0.83[CEU][hapmap]
rs681639	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693436	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524286	0.95[CHB][hapmap]
rs7536101	0.89[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap]
rs861933	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3340591	chr1:86439980-86459810	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs482789	LOC339524	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86449400-86466200	Weak transcription	Fetal Lung	lung
2	chr1:86451400-86455600	Weak transcription	GM12878-XiMat	blood
3	chr1:86451600-86455000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:86452200-86455600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:86452600-86453000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:86452600-86453200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:86452800-86453200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links