Variant report

Variant	rs12107272
Chromosome Location	chr3:98698202-98698203
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10428160	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10589669	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11552978	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12108018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12108142	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13059624	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13065136	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13068317	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13072410	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13074614	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13074787	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13076960	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13078549	0.91[EUR][1000 genomes]
rs13079960	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13080057	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13081992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13083238	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083613	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13083934	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13084692	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13087627	0.95[EUR][1000 genomes]
rs13087631	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13088532	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13091170	0.95[EUR][1000 genomes]
rs13091236	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13091956	0.84[EUR][1000 genomes]
rs13093128	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13096085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13097876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13100915	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13100937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1983009	0.82[EUR][1000 genomes]
rs2439232	0.89[EUR][1000 genomes]
rs2454687	0.91[EUR][1000 genomes]
rs34008360	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34269725	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34279227	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34284740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34394867	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34428696	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs34470469	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34479374	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34489202	0.95[EUR][1000 genomes]
rs34688367	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34711372	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34725039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34826460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34848749	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34860591	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35006699	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35025156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35076733	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs35098355	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35103318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35219252	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35234681	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35239055	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35312318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35366262	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35422064	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35499232	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35514544	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35526367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35539438	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35592768	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35764973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35854439	0.84[EUR][1000 genomes]
rs35894621	0.82[EUR][1000 genomes]
rs35914268	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35947493	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35947806	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36032715	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36098932	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36157152	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36160001	0.86[EUR][1000 genomes]
rs36175276	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs41267851	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55644421	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56083233	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56094988	0.91[AMR][1000 genomes]
rs56246599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56408882	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6764579	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6805362	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71124004	0.81[EUR][1000 genomes]
rs71311393	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71311394	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71311397	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311398	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71311402	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313504	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71313506	0.93[EUR][1000 genomes]
rs71313508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7614053	1.00[AMR][1000 genomes];0.98[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	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking 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	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98692000-98699600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr3:98695400-98698800	Enhancers	Osteobl	bone
3	chr3:98696000-98699600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:98696400-98699000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:98696400-98699800	Enhancers	GM12878-XiMat	blood
6	chr3:98696600-98698800	Enhancers	NH-A	brain
7	chr3:98696600-98699800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:98696800-98699000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:98696800-98700400	Enhancers	HUVEC	blood vessel
10	chr3:98697000-98699600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:98697000-98699800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:98697000-98699800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:98697000-98700000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:98697200-98699800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:98697200-98700000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:98697200-98705000	Weak transcription	HSMMtube	muscle
17	chr3:98697400-98698400	Weak transcription	HepG2	liver
18	chr3:98697400-98699000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:98697400-98699800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:98697600-98699000	Weak transcription	NHEK	skin
21	chr3:98697600-98699600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:98697600-98699600	Weak transcription	HSMM	muscle
23	chr3:98697600-98700000	Weak transcription	Hela-S3	cervix
24	chr3:98697800-98699600	Weak transcription	HMEC	breast
25	chr3:98697800-98699800	Weak transcription	NHLF	lung
26	chr3:98698000-98699000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:98698000-98700000	Enhancers	NHDF-Ad	bronchial
28	chr3:98698200-98699000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:98698200-98699000	Enhancers	A549	lung

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