Variant report

Variant	rs62001731
Chromosome Location	chr15:58661545-58661546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10518973	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11854016	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11855842	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12148283	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12324273	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12324543	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16940116	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2115907	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28842782	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62001709	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62001710	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62001712	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62001732	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68077377	0.80[EUR][1000 genomes]
rs8042092	0.87[AMR][1000 genomes];0.83[EUR][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	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv904266	chr15:58580921-58689187	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1041779	chr15:58634768-58662280	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58656000-58663600	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr15:58656200-58661600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:58656400-58661600	Weak transcription	Primary T cells from cord blood	blood
4	chr15:58656400-58661600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:58661200-58662400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:58661200-58662400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:58661200-58662400	Enhancers	Liver	Liver
8	chr15:58661400-58661600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:58661400-58661600	Flanking Active TSS	Fetal Kidney	kidney
10	chr15:58661400-58661600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr15:58661400-58661600	Flanking Active TSS	Osteobl	bone
12	chr15:58661400-58661800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr15:58661400-58661800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr15:58661400-58661800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr15:58661400-58661800	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr15:58661400-58661800	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr15:58661400-58662000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:58661400-58662000	Active TSS	GM12878-XiMat	blood
19	chr15:58661400-58662000	Active TSS	HepG2	liver
20	chr15:58661400-58662200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:58661400-58662200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:58661400-58662200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:58661400-58662200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:58661400-58662400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr15:58661400-58662400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:58661400-58662400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:58661400-58662400	Enhancers	Fetal Thymus	thymus
28	chr15:58661400-58662400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr15:58661400-58662400	Enhancers	HSMMtube	muscle
30	chr15:58661400-58662800	Enhancers	HSMM	muscle

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