Variant report

Variant	rs17398421
Chromosome Location	chr3:100672907-100672908
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1036467	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10511181	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13060137	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13060166	0.89[EUR][1000 genomes]
rs13072000	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs13072788	0.91[EUR][1000 genomes]
rs13077353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13079002	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs13080859	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13088524	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13091757	0.89[EUR][1000 genomes]
rs13092605	0.85[EUR][1000 genomes]
rs13099053	0.87[EUR][1000 genomes]
rs13100301	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17284842	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17338506	0.85[CEU][hapmap]
rs17398684	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17399603	0.91[EUR][1000 genomes]
rs2245266	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2245473	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs2245556	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2576365	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs2576369	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2576372	0.89[EUR][1000 genomes]
rs2576377	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2576382	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2576387	0.87[EUR][1000 genomes]
rs2576391	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2595893	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2595894	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713748	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2713764	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2713782	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs2713786	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713787	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2713788	0.82[EUR][1000 genomes]
rs2713789	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs2713793	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs34275644	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34315591	0.89[EUR][1000 genomes]
rs34515751	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34565718	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34645172	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34719725	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34897295	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34999788	0.84[EUR][1000 genomes]
rs35509049	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35517882	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35530876	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35617051	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35630894	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35974360	0.86[EUR][1000 genomes]
rs35999953	0.85[EUR][1000 genomes]
rs36156426	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36165056	0.85[EUR][1000 genomes]
rs36194526	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4060963	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs41273553	0.87[EUR][1000 genomes]
rs41386544	0.86[EUR][1000 genomes]
rs4928096	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs62273925	0.90[EUR][1000 genomes]
rs62273927	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62273928	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62273930	0.94[EUR][1000 genomes]
rs62273935	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62275197	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62275198	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62275199	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62275200	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62275203	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62275204	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62275770	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62275773	0.91[EUR][1000 genomes]
rs62275774	0.85[EUR][1000 genomes]
rs62275825	0.86[EUR][1000 genomes]
rs6441552	1.00[CHD][hapmap]
rs66852780	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67946790	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67991823	0.87[EUR][1000 genomes]
rs73137276	0.80[EUR][1000 genomes]
rs73143088	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7431835	1.00[CEU][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes]
rs9832195	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs9840644	0.85[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2422136	chr3:100669517-100673226	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv441834	chr3:100669517-100673226	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100630200-100673600	Weak transcription	Ovary	ovary
2	chr3:100660600-100673200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:100660600-100673600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:100660600-100673600	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:100667000-100675600	Weak transcription	Aorta	Aorta
6	chr3:100667400-100673400	Weak transcription	Fetal Stomach	stomach
7	chr3:100671600-100673200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:100671800-100674000	Enhancers	HSMMtube	muscle
9	chr3:100671800-100677200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:100672200-100673600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:100672200-100675200	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:100672200-100677200	Enhancers	NHDF-Ad	bronchial
13	chr3:100672400-100673200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:100672600-100673200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:100672600-100677200	Enhancers	Osteobl	bone
16	chr3:100672800-100674000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:100672800-100674200	Enhancers	HSMM	muscle
18	chr3:100672800-100674200	Enhancers	HUVEC	blood vessel
19	chr3:100672800-100674600	Enhancers	NHEK	skin

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