Variant report

Variant	rs12139369
Chromosome Location	chr1:103594551-103594552
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10159431	0.81[ASN][1000 genomes]
rs10399857	0.81[ASN][1000 genomes]
rs10437029	0.95[ASN][1000 genomes]
rs10874680	0.87[ASN][1000 genomes]
rs10874681	1.00[ASN][1000 genomes]
rs10874682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874684	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874685	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874686	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10874687	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874688	1.00[ASN][1000 genomes]
rs10874694	0.81[ASN][1000 genomes]
rs11164673	0.89[ASN][1000 genomes]
rs11164676	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164683	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164684	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164686	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11164690	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164694	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11164706	0.95[ASN][1000 genomes]
rs11164711	0.85[ASN][1000 genomes]
rs11164715	0.81[ASN][1000 genomes]
rs11164716	0.81[ASN][1000 genomes]
rs11164717	0.81[ASN][1000 genomes]
rs11802357	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810850	0.81[ASN][1000 genomes]
rs12075533	0.90[ASN][1000 genomes]
rs12077815	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12078066	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12090752	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094089	0.95[ASN][1000 genomes]
rs12119790	0.81[ASN][1000 genomes]
rs12125839	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126095	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12126147	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131628	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12134283	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134285	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136163	0.81[AFR][1000 genomes]
rs12139417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140409	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142507	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12142969	0.95[ASN][1000 genomes]
rs12143615	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143640	0.81[AFR][1000 genomes]
rs1337171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337198	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1337199	0.97[ASN][1000 genomes]
rs13374757	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13375484	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358459	0.90[ASN][1000 genomes]
rs1406127	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1406129	0.90[ASN][1000 genomes]
rs1538039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572517	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572519	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572520	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1577806	0.97[ASN][1000 genomes]
rs17127531	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1852655	0.90[ASN][1000 genomes]
rs2178162	0.81[ASN][1000 genomes]
rs2889340	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850460	0.97[ASN][1000 genomes]
rs3850461	0.97[ASN][1000 genomes]
rs3850462	0.97[ASN][1000 genomes]
rs3861744	0.97[ASN][1000 genomes]
rs4098281	1.00[ASN][1000 genomes]
rs4332376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55926955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335123	0.85[ASN][1000 genomes]
rs56350510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57003205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59026756	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814997	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61814998	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61814999	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61815034	0.95[ASN][1000 genomes]
rs61815035	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61815037	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61815038	0.95[ASN][1000 genomes]
rs6577358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6577361	0.97[ASN][1000 genomes]
rs6577362	0.95[ASN][1000 genomes]
rs6577363	0.83[ASN][1000 genomes]
rs6657840	0.90[ASN][1000 genomes]
rs6658609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660886	0.95[ASN][1000 genomes]
rs6665601	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6670472	0.95[ASN][1000 genomes]
rs6670951	0.95[ASN][1000 genomes]
rs6673525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674625	0.85[ASN][1000 genomes]
rs6675440	0.97[ASN][1000 genomes]
rs6678780	0.95[ASN][1000 genomes]
rs6681533	1.00[ASN][1000 genomes]
rs6699034	0.81[ASN][1000 genomes]
rs6701783	0.90[ASN][1000 genomes]
rs6703986	0.95[ASN][1000 genomes]
rs6704272	0.90[ASN][1000 genomes]
rs7411801	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515978	0.97[ASN][1000 genomes]
rs7518542	0.97[ASN][1000 genomes]
rs7519151	0.97[ASN][1000 genomes]
rs7520070	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7523058	0.97[ASN][1000 genomes]
rs7524445	0.95[ASN][1000 genomes]
rs7526605	0.85[ASN][1000 genomes]
rs7534313	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534696	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544745	1.00[ASN][1000 genomes]
rs7550030	0.93[ASN][1000 genomes]
rs7555795	0.95[ASN][1000 genomes]
rs872317	0.97[ASN][1000 genomes]
rs9651143	0.81[ASN][1000 genomes]
rs9651144	0.81[ASN][1000 genomes]
rs9651151	0.81[ASN][1000 genomes]
rs9662902	0.90[ASN][1000 genomes]
rs9663072	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv522922	chr1:103305021-103764640	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830893	chr1:103458498-103635579	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931600	chr1:103548397-104161031	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv498007	chr1:103573857-104107589	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:103593800-103594800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:103593800-103595200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:103594200-103595200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:103594200-103595400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:103594400-103595200	Enhancers	Osteobl	bone
6	chr1:103594400-103595600	Enhancers	HSMM	muscle
7	chr1:103594400-103595800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:103594400-103596000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:103594400-103596000	Enhancers	HSMMtube	muscle

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