Variant report

Variant	rs12049259
Chromosome Location	chr1:78916317-78916318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10082040	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10489785	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs10782664	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs10782665	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10873979	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10873980	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs10873983	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873984	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873985	0.81[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11162477	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs11162479	0.91[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs11162488	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162489	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162490	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11162492	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11162493	0.90[ASN][1000 genomes]
rs1156031	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs12024476	0.90[ASN][1000 genomes]
rs12031857	0.95[ASN][1000 genomes]
rs12073895	0.90[ASN][1000 genomes]
rs12122274	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs12128334	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12132664	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs12141234	0.84[EUR][1000 genomes]
rs12717769	0.88[EUR][1000 genomes]
rs12733301	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs12740373	0.86[EUR][1000 genomes]
rs12742293	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs12752083	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[EUR][1000 genomes]
rs1328447	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs1328448	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1332254	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1333069	0.80[EUR][1000 genomes]
rs1333070	0.88[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes]
rs1333071	0.86[CEU][hapmap];0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs1543675	0.91[JPT][hapmap]
rs1571366	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1576806	0.90[ASN][1000 genomes]
rs1581749	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1590312	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1590313	0.91[ASN][1000 genomes]
rs1831168	0.95[CHB][hapmap]
rs1929982	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2208897	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2224674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2990698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35166559	0.95[ASN][1000 genomes]
rs4587523	0.88[EUR][1000 genomes]
rs4650348	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[EUR][1000 genomes]
rs4650549	0.86[JPT][hapmap]
rs473910	0.92[CEU][hapmap];0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs482493	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs490938	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs494981	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs508404	0.82[ASN][1000 genomes]
rs521636	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs523464	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs525351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs537086	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs538855	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs555475	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs571456	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs583964	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs585795	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs587996	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs591889	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs595489	0.80[EUR][1000 genomes]
rs604097	0.81[EUR][1000 genomes]
rs626063	0.81[EUR][1000 genomes]
rs631280	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs639594	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs646012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648425	0.83[YRI][hapmap]
rs648572	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs651313	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs663934	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6678699	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs678443	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs689294	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7541577	0.84[EUR][1000 genomes]
rs789283	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv482697	chr1:78786028-78935333	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870807	chr1:78867347-79032598	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78907800-78927200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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