Variant report

Variant	rs7138401
Chromosome Location	chr12:59379529-59379530
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	chr12:59379293..59381113-chr12:59382068..59383913,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10506357	1.00[AFR][1000 genomes]
rs10877188	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10877198	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877200	0.93[EUR][1000 genomes]
rs10877203	1.00[AFR][1000 genomes]
rs11172823	0.82[EUR][1000 genomes]
rs11172824	0.82[EUR][1000 genomes]
rs11172825	0.82[EUR][1000 genomes]
rs11172827	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172831	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172833	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172837	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172839	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172840	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172846	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172857	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172858	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172860	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172861	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172862	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11172866	0.93[EUR][1000 genomes]
rs11172867	0.93[EUR][1000 genomes]
rs11172868	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs11172869	0.84[EUR][1000 genomes]
rs11172870	0.86[EUR][1000 genomes]
rs11172873	1.00[AFR][1000 genomes]
rs11172874	1.00[AFR][1000 genomes]
rs11172876	1.00[AFR][1000 genomes]
rs11172878	1.00[AFR][1000 genomes]
rs11172880	1.00[AFR][1000 genomes]
rs11172881	1.00[AFR][1000 genomes]
rs11172882	1.00[AFR][1000 genomes]
rs11172888	1.00[AFR][1000 genomes]
rs11172891	1.00[AFR][1000 genomes]
rs11172898	1.00[AFR][1000 genomes]
rs12367126	1.00[AFR][1000 genomes]
rs12368035	1.00[AFR][1000 genomes]
rs12368752	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12369750	0.82[EUR][1000 genomes]
rs12370707	1.00[AFR][1000 genomes]
rs12371014	1.00[AFR][1000 genomes]
rs12423502	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12424788	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12425735	1.00[AFR][1000 genomes]
rs12426212	0.81[EUR][1000 genomes]
rs12426969	0.82[EUR][1000 genomes]
rs17121828	0.93[EUR][1000 genomes]
rs17536893	1.00[AFR][1000 genomes]
rs17537939	1.00[AFR][1000 genomes]
rs17627506	1.00[AFR][1000 genomes]
rs2120527	1.00[AFR][1000 genomes]
rs55888651	0.93[EUR][1000 genomes]
rs58692617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60522760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60984323	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61754220	0.82[EUR][1000 genomes]
rs61919461	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61919462	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919464	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919465	0.89[EUR][1000 genomes]
rs61919466	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919469	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919471	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919513	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919518	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919520	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919521	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919523	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919524	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61919525	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919531	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs61919532	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs61919550	1.00[AFR][1000 genomes]
rs61934309	1.00[AFR][1000 genomes]
rs6581224	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7136193	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7294684	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7297094	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301299	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302365	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303773	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7309872	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7314727	1.00[AFR][1000 genomes]
rs7963207	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968111	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969722	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7970054	0.84[EUR][1000 genomes]
rs7980136	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7980483	0.82[EUR][1000 genomes]
rs9645802	0.87[AMR][1000 genomes];0.89[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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv559048	chr12:59336737-59440659	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv559049	chr12:59359937-59436179	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59377800-59381200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:59379400-59379600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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