Variant report

Variant	rs12089449
Chromosome Location	chr1:210269108-210269109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1040424	1.00[AFR][1000 genomes]
rs1040426	1.00[AFR][1000 genomes]
rs10489346	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10779520	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10779521	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10863796	1.00[EUR][1000 genomes]
rs10863800	1.00[AFR][1000 genomes]
rs10863801	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10863806	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10863809	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs10863814	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11119360	1.00[EUR][1000 genomes]
rs11119361	1.00[EUR][1000 genomes]
rs11119362	1.00[EUR][1000 genomes]
rs11119371	0.80[CHB][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11119372	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119373	1.00[AFR][1000 genomes]
rs11119384	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11119388	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11119391	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119394	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11119398	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11119401	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119403	0.93[AMR][1000 genomes]
rs11119417	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11119433	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119434	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11119442	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12057832	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059828	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12061641	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12062530	0.84[AMR][1000 genomes]
rs12064990	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12065575	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066358	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067807	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12069592	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073617	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12078802	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12079812	1.00[EUR][1000 genomes]
rs12079916	0.97[AMR][1000 genomes]
rs12083219	1.00[AFR][1000 genomes]
rs12084199	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12085177	0.81[AMR][1000 genomes]
rs12088422	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12089327	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12092527	0.98[AMR][1000 genomes]
rs12094309	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094626	0.81[AMR][1000 genomes]
rs12354000	1.00[AFR][1000 genomes]
rs12401574	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403002	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12405519	1.00[AFR][1000 genomes]
rs12405601	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12406136	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12407647	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12408689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409047	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12409060	1.00[AFR][1000 genomes]
rs12409069	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12409582	0.80[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes]
rs12565072	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12566105	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12566314	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12569033	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1338297	1.00[AFR][1000 genomes]
rs1387932	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17015564	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17015565	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17015566	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17015667	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs2130625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2130629	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs2273047	1.00[EUR][1000 genomes]
rs28417505	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4844498	1.00[EUR][1000 genomes]
rs4844501	1.00[AFR][1000 genomes]
rs4844507	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844509	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs4844916	1.00[AFR][1000 genomes]
rs4844923	1.00[AFR][1000 genomes]
rs4844924	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4844928	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844935	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4844936	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4844937	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4844938	0.82[AMR][1000 genomes]
rs4844939	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4844940	0.82[AMR][1000 genomes]
rs4844941	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4844942	0.90[AMR][1000 genomes]
rs4844943	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844944	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844945	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4844946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4844955	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs713114	1.00[AFR][1000 genomes]
rs72649921	1.00[AFR][1000 genomes]
rs72649923	1.00[AFR][1000 genomes]
rs72649924	1.00[AFR][1000 genomes]
rs72649925	1.00[AFR][1000 genomes]
rs72649937	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs72649938	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72649940	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72649948	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649949	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649955	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs72649956	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649959	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649960	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs72649964	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72649967	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72649968	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72649969	1.00[AFR][1000 genomes]
rs7416285	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs760768	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9787400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9919217	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	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
8	nsv818800	chr1:210258653-210304319	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210248600-210273200	Weak transcription	Fetal Brain Female	brain
2	chr1:210250800-210278800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210257800-210275000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:210260600-210285200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:210262000-210279600	Weak transcription	NH-A	brain
6	chr1:210263200-210269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:210266400-210279000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:210268000-210269400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:210268400-210287400	Weak transcription	Brain Germinal Matrix	brain
10	chr1:210269000-210278400	Weak transcription	Brain Inferior Temporal Lobe	brain

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