Variant report

Variant	rs12088422
Chromosome Location	chr1:210343435-210343436
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	chr1:210338675..210341469-chr1:210342023..210343618,2	MCF-7	breast:

Extended variants
information (count: 140 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1040424	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1040426	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10489346	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10779520	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10779521	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863800	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10863801	1.00[AFR][1000 genomes]
rs10863806	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10863809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11119373	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11119384	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11119388	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11119391	1.00[AFR][1000 genomes]
rs11119394	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119398	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119401	0.89[AMR][1000 genomes]
rs11119403	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119415	0.84[ASN][1000 genomes]
rs11119417	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11119419	0.87[ASN][1000 genomes]
rs11119420	0.84[ASN][1000 genomes]
rs11119433	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11119434	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11119442	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12057832	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12059828	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061641	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12062530	0.90[AMR][1000 genomes]
rs12064990	1.00[AFR][1000 genomes]
rs12065575	1.00[AFR][1000 genomes]
rs12066358	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12067807	1.00[AFR][1000 genomes]
rs12073617	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078802	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12079916	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12083219	1.00[AFR][1000 genomes]
rs12084199	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12089327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12089449	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12092527	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094309	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12094626	1.00[EUR][1000 genomes]
rs12401574	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12403002	1.00[AFR][1000 genomes]
rs12403098	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12405519	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12405601	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12406136	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12408689	0.93[AMR][1000 genomes]
rs12409047	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12409060	1.00[AFR][1000 genomes]
rs12409069	0.90[AMR][1000 genomes]
rs12409582	1.00[AFR][1000 genomes]
rs12561877	0.87[EUR][1000 genomes]
rs12565072	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12565234	0.87[EUR][1000 genomes]
rs12566105	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566314	1.00[AFR][1000 genomes]
rs12567184	0.87[EUR][1000 genomes]
rs12567185	0.87[EUR][1000 genomes]
rs12569033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1338297	1.00[AFR][1000 genomes]
rs1387932	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015564	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015565	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015566	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17015667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2130625	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2130629	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2151940	0.81[ASN][1000 genomes]
rs28417505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4144930	0.87[EUR][1000 genomes]
rs4589111	1.00[AFR][1000 genomes]
rs4844507	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4844509	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844923	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4844924	1.00[AFR][1000 genomes]
rs4844928	1.00[AFR][1000 genomes]
rs4844935	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4844936	1.00[AFR][1000 genomes]
rs4844937	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844938	1.00[EUR][1000 genomes]
rs4844939	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844940	1.00[EUR][1000 genomes]
rs4844941	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844942	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844943	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844944	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844945	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4844946	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844950	0.89[ASN][1000 genomes]
rs4844955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713114	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72649922	0.87[EUR][1000 genomes]
rs72649923	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72649924	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72649925	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72649926	0.87[EUR][1000 genomes]
rs72649928	0.87[EUR][1000 genomes]
rs72649929	0.87[EUR][1000 genomes]
rs72649930	0.87[EUR][1000 genomes]
rs72649931	0.87[EUR][1000 genomes]
rs72649932	0.87[EUR][1000 genomes]
rs72649933	0.87[EUR][1000 genomes]
rs72649934	0.87[EUR][1000 genomes]
rs72649935	0.87[EUR][1000 genomes]
rs72649936	0.87[EUR][1000 genomes]
rs72649937	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649938	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649939	0.87[EUR][1000 genomes]
rs72649940	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649941	0.87[EUR][1000 genomes]
rs72649942	0.87[EUR][1000 genomes]
rs72649944	0.87[EUR][1000 genomes]
rs72649945	0.87[EUR][1000 genomes]
rs72649946	0.87[EUR][1000 genomes]
rs72649947	0.87[EUR][1000 genomes]
rs72649948	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649949	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649950	0.87[EUR][1000 genomes]
rs72649951	0.87[EUR][1000 genomes]
rs72649953	0.87[EUR][1000 genomes]
rs72649954	0.87[EUR][1000 genomes]
rs72649955	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72649956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72649958	0.87[EUR][1000 genomes]
rs72649959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649964	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72649967	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649968	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649969	1.00[AFR][1000 genomes]
rs7416285	1.00[AFR][1000 genomes]
rs760768	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9787400	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv873144	chr1:210252522-210347417	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv873145	chr1:210302595-210347417	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv873146	chr1:210312760-210347417	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210339400-210361200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210341000-210344200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr1:210343400-210345000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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