Variant report

Variant	rs13079002
Chromosome Location	chr3:100630141-100630142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IMPG2-2	chr3:100629819-100631019	NONHSAT090881

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1036467	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10511181	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs13060137	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs13072000	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13077353	0.85[CEU][hapmap];0.92[EUR][1000 genomes]
rs13080859	0.86[EUR][1000 genomes]
rs13088524	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs13092605	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13099053	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13100301	0.92[EUR][1000 genomes]
rs17284842	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs17338506	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17398421	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs17398684	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2245266	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2245473	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2245556	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2576365	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576369	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576372	0.98[EUR][1000 genomes]
rs2576377	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs2576382	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2576387	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576391	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs2595893	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2595894	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs2713748	0.85[EUR][1000 genomes]
rs2713764	0.89[EUR][1000 genomes]
rs2713782	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2713786	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2713787	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713788	0.94[EUR][1000 genomes]
rs2713789	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713793	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34275644	0.89[EUR][1000 genomes]
rs34315591	0.91[EUR][1000 genomes]
rs34515751	0.89[EUR][1000 genomes]
rs34565718	0.92[EUR][1000 genomes]
rs34645172	0.82[EUR][1000 genomes]
rs34719725	0.87[EUR][1000 genomes]
rs34999788	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35090886	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35509049	0.87[EUR][1000 genomes]
rs35517882	0.83[EUR][1000 genomes]
rs35530876	0.87[EUR][1000 genomes]
rs35617051	0.86[EUR][1000 genomes]
rs35630894	0.87[EUR][1000 genomes]
rs35999953	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36156426	0.92[EUR][1000 genomes]
rs36165056	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36194526	0.89[EUR][1000 genomes]
rs4060963	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41273553	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4928096	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs62273925	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62273927	0.92[EUR][1000 genomes]
rs62273928	0.92[EUR][1000 genomes]
rs62273930	0.89[EUR][1000 genomes]
rs62273935	0.87[EUR][1000 genomes]
rs62275197	0.87[EUR][1000 genomes]
rs62275198	0.87[EUR][1000 genomes]
rs62275199	0.85[EUR][1000 genomes]
rs62275200	0.85[EUR][1000 genomes]
rs62275203	0.82[EUR][1000 genomes]
rs62275204	0.82[EUR][1000 genomes]
rs62277105	0.86[EUR][1000 genomes]
rs66852780	0.82[EUR][1000 genomes]
rs67946790	0.87[EUR][1000 genomes]
rs67991823	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72928364	0.82[EUR][1000 genomes]
rs73137256	0.86[EUR][1000 genomes]
rs73137276	0.90[EUR][1000 genomes]
rs73143088	0.87[EUR][1000 genomes]
rs7431835	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs9832195	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9840644	0.91[AMR][1000 genomes];0.98[EUR][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	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
3	chr3:100617600-100641000	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:100617800-100641000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:100621600-100633400	Weak transcription	HSMMtube	muscle
6	chr3:100622000-100631800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:100623200-100631800	Weak transcription	NHDF-Ad	bronchial
8	chr3:100629600-100630400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:100629600-100630400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:100629600-100630400	Enhancers	Osteobl	bone
11	chr3:100629600-100630600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:100629800-100630200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:100629800-100630200	Enhancers	HSMM	muscle
14	chr3:100629800-100631800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:100630000-100630200	Enhancers	Ovary	ovary
16	chr3:100630000-100630200	Enhancers	NHLF	lung
17	chr3:100630000-100630800	Weak transcription	Stomach Smooth Muscle	stomach

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