Variant report

Variant	rs12059828
Chromosome Location	chr1:210247222-210247223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs1040424	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1040425	0.85[ASN][1000 genomes]
rs1040426	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10489346	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10779520	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10779521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863800	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10863801	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10863806	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10863809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863814	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11119371	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11119372	0.85[AMR][1000 genomes]
rs11119373	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11119384	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11119388	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11119391	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11119394	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119398	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119401	0.98[AMR][1000 genomes]
rs11119403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11119417	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119433	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11119434	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11119442	1.00[AFR][1000 genomes]
rs12057832	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12061641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12062530	0.81[AMR][1000 genomes]
rs12064990	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12065575	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12066358	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12067807	1.00[AFR][1000 genomes]
rs12069592	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12073617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12078802	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12079916	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12083219	1.00[AFR][1000 genomes]
rs12084199	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12085177	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12088422	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12089327	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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];0.82[ASN][1000 genomes]
rs12094309	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12094626	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12354000	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12401574	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12403002	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12403098	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12405519	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12405601	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12406136	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12407647	0.84[AMR][1000 genomes]
rs12408689	0.93[AMR][1000 genomes]
rs12409047	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12409060	1.00[AFR][1000 genomes]
rs12409069	0.90[AMR][1000 genomes]
rs12409582	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12561877	0.87[EUR][1000 genomes]
rs12565072	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565234	0.87[EUR][1000 genomes]
rs12565533	0.87[EUR][1000 genomes]
rs12566105	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12566314	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12567184	0.87[EUR][1000 genomes]
rs12567185	0.87[EUR][1000 genomes]
rs12569033	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12569195	0.87[EUR][1000 genomes]
rs1338297	1.00[AFR][1000 genomes]
rs1387932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015667	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2130625	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2130629	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2151940	0.83[ASN][1000 genomes]
rs28417505	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4144930	0.87[EUR][1000 genomes]
rs4844501	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844502	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844507	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4844509	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844916	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844923	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4844924	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4844928	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4844935	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844936	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4844937	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844938	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4844939	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844940	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4844941	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844942	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4844943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4844944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4844945	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4844946	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844955	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs713114	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72649911	0.87[EUR][1000 genomes]
rs72649912	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649913	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649914	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649920	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649921	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649922	0.87[EUR][1000 genomes]
rs72649923	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72649924	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72649925	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72649938	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72649939	0.87[EUR][1000 genomes]
rs72649940	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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]
rs72649956	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649958	0.87[EUR][1000 genomes]
rs72649959	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649960	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72649964	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72649967	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72649968	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72649969	1.00[AFR][1000 genomes]
rs7416285	1.00[AFR][1000 genomes]
rs760768	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9787400	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs9919217	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv873141	chr1:210228131-210296910	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv873142	chr1:210233610-210291121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv873143	chr1:210233610-210296910	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210224400-210250000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210244200-210248400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:210244400-210250000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:210245200-210247600	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr1:210245600-210248000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr1:210245600-210248400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:210245600-210248600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:210245600-210248600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:210245600-210248600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:210245800-210247600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:210246200-210250000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:210246400-210248200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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