Variant report

Variant	rs2562343
Chromosome Location	chr5:16892404-16892405
allele	A/G
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:9)

rs_ID	r²[population]
rs253483	0.87[AMR][1000 genomes]
rs2560846	0.80[AMR][1000 genomes]
rs2560850	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560851	0.83[CHB][hapmap]
rs2562339	0.85[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562347	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562353	0.82[AMR][1000 genomes]
rs2625174	0.80[AMR][1000 genomes]
rs2625175	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762500	chr5:16815489-16952565	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv1034844	chr5:16854341-16903100	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3485757	chr5:16856475-16966851	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	esv3485758	chr5:16856475-16966851	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16874000-16894600	Weak transcription	Esophagus	oesophagus
2	chr5:16878200-16893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:16880600-16894800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:16882000-16894200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:16882800-16895600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:16884400-16894800	Weak transcription	Psoas Muscle	Psoas
7	chr5:16885400-16894200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:16886000-16893600	Weak transcription	Colonic Mucosa	Colon
9	chr5:16886200-16894400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:16887200-16894000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:16887400-16894200	Weak transcription	Placenta	Placenta
12	chr5:16887600-16894200	Weak transcription	Adipose Nuclei	Adipose
13	chr5:16888600-16893000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:16888600-16893000	Enhancers	Duodenum Mucosa	Duodenum
15	chr5:16888600-16894200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr5:16888800-16892800	Enhancers	Pancreas	Pancrea
17	chr5:16889400-16892600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr5:16889800-16894000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:16890000-16894200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:16890200-16892600	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr5:16890200-16894200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:16890200-16894600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:16890400-16894600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr5:16890400-16894600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:16890400-16894800	Weak transcription	Fetal Stomach	stomach
26	chr5:16890600-16892800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:16890600-16893800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:16890600-16893800	Weak transcription	Stomach Mucosa	stomach
29	chr5:16890600-16894000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:16890600-16894000	Weak transcription	NH-A	brain
31	chr5:16890600-16894000	Weak transcription	Osteobl	bone
32	chr5:16890600-16894400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr5:16890600-16894400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:16890600-16894600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:16890800-16893800	Enhancers	Hela-S3	cervix
36	chr5:16890800-16894000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:16890800-16894200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:16890800-16894200	Weak transcription	HSMMtube	muscle
39	chr5:16891000-16892800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:16891200-16892600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:16891200-16893800	Weak transcription	HMEC	breast
42	chr5:16891200-16894000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr5:16891200-16894200	Weak transcription	HSMM	muscle
44	chr5:16891200-16894200	Weak transcription	NHDF-Ad	bronchial
45	chr5:16891400-16892600	Enhancers	Small Intestine	intestine
46	chr5:16891400-16893800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:16891400-16894000	Weak transcription	NHEK	skin
48	chr5:16891400-16894200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr5:16891400-16894200	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:16891400-16894800	Weak transcription	Ovary	ovary

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