Variant report

Variant	rs12909642
Chromosome Location	chr15:58754497-58754498
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17301781	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1869143	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs34838631	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34959352	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1043362	chr15:58726337-58756571	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv457173	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv569600	chr15:58731567-58779039	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58737400-58761800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:58743800-58770400	Enhancers	Fetal Thymus	thymus
3	chr15:58747600-58754800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:58748400-58755000	Weak transcription	Gastric	stomach
5	chr15:58749600-58755600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:58749600-58756000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr15:58751200-58757200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:58751600-58757800	Weak transcription	Fetal Kidney	kidney
9	chr15:58752000-58754600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:58752000-58755200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:58752000-58757800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:58752000-58757800	Weak transcription	NHLF	lung
13	chr15:58752200-58754600	Weak transcription	Liver	Liver
14	chr15:58752200-58755000	Weak transcription	Esophagus	oesophagus
15	chr15:58752200-58755000	Weak transcription	K562	blood
16	chr15:58752200-58755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:58752400-58754800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:58752400-58755200	Weak transcription	Small Intestine	intestine
19	chr15:58752400-58756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:58752400-58761800	Weak transcription	Right Atrium	heart
21	chr15:58752600-58755000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr15:58752600-58760200	Weak transcription	Hela-S3	cervix
23	chr15:58752800-58754600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr15:58752800-58754600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:58752800-58754600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:58752800-58754600	Weak transcription	Fetal Intestine Small	intestine
27	chr15:58752800-58754600	Weak transcription	A549	lung
28	chr15:58752800-58754800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:58752800-58754800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:58752800-58755200	Weak transcription	Dnd41	blood
31	chr15:58752800-58755400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:58752800-58757800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:58752800-58757800	Weak transcription	HSMM	muscle
34	chr15:58752800-58765000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:58753000-58754600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:58753000-58754800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:58753000-58754800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr15:58753000-58755200	Weak transcription	HSMMtube	muscle
39	chr15:58753000-58760400	Weak transcription	Pancreas	Pancrea
40	chr15:58753200-58754800	Weak transcription	Placenta	Placenta
41	chr15:58753200-58755000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:58753400-58754800	Weak transcription	Fetal Muscle Leg	muscle
43	chr15:58753400-58754800	Weak transcription	GM12878-XiMat	blood
44	chr15:58753400-58756000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:58753600-58755000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:58753600-58755400	Enhancers	Colonic Mucosa	Colon
47	chr15:58753800-58755800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr15:58753800-58757000	Enhancers	Thymus	Thymus
49	chr15:58754000-58755400	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr15:58754000-58759400	Enhancers	HepG2	liver

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