Variant report

Variant	rs1962605
Chromosome Location	chr4:78300489-78300490
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	chr4:78298658..78300930-chr4:78308885..78310955,2	MCF-7	breast:
2	chr4:78289830..78292754-chr4:78299148..78300754,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10010842	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10013386	0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10015193	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10018010	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10031809	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518179	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs10518180	0.90[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11724731	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933902	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11941858	0.95[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs11946669	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12504998	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1372784	0.90[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs1372785	0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs1372786	0.94[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap]
rs1545252	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1545253	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs17002668	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs1837968	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1962026	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216629	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2866281	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2866282	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866284	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2866285	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827478	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28858493	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36076516	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4282207	0.83[ASW][hapmap]
rs4359931	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4579145	0.83[ASW][hapmap]
rs4579146	0.90[CEU][hapmap]
rs4859492	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859493	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859824	0.90[CEU][hapmap];0.80[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs4859827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859831	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859832	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859833	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4859834	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56403473	0.85[ASN][1000 genomes]
rs6533028	0.90[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs6533029	0.90[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs66500830	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6817200	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6825194	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6831412	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6832575	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs6843922	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6856470	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7375525	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap]
rs7375603	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap]
rs7378081	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs7679224	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7695467	0.83[ASW][hapmap]
rs7699246	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs894433	0.86[CEU][hapmap]
rs894434	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9307275	0.89[CEU][hapmap];0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1010450	chr4:78182037-78317840	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1004824	chr4:78188691-78312974	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1845782	chr4:78237955-78321598	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1000392	chr4:78273146-78301467	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1011607	chr4:78273146-78302096	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3442840	chr4:78277532-78309591	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv594698	chr4:78291876-78334483	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78298400-78306800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:78299400-78300600	Enhancers	Fetal Intestine Large	intestine
3	chr4:78299600-78300600	Enhancers	Fetal Intestine Small	intestine

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