Variant report

Variant	rs2562340
Chromosome Location	chr5:16887009-16887010
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10035649	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12513932	0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2560851	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2562341	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562342	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2625166	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2625167	0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2625168	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2625169	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28696289	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16867600-16889000	Weak transcription	Spleen	Spleen
2	chr5:16874000-16894600	Weak transcription	Esophagus	oesophagus
3	chr5:16875600-16889000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:16877400-16888200	Weak transcription	HUVEC	blood vessel
5	chr5:16877400-16889000	Weak transcription	Fetal Stomach	stomach
6	chr5:16877800-16889000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:16878200-16893800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:16879600-16887600	Enhancers	HSMM	muscle
9	chr5:16880600-16894800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:16881000-16889800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:16881800-16888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:16881800-16889000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:16881800-16889000	Weak transcription	Fetal Kidney	kidney
14	chr5:16881800-16889400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:16881800-16889800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:16882000-16894200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:16882400-16889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:16882600-16888800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:16882600-16889800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:16882800-16895600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:16883400-16887200	Enhancers	Ovary	ovary
22	chr5:16883400-16887600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:16883400-16889400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:16884000-16887400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:16884000-16887600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:16884000-16887600	Enhancers	Fetal Muscle Leg	muscle
27	chr5:16884000-16888200	Enhancers	Fetal Lung	lung
28	chr5:16884400-16894800	Weak transcription	Psoas Muscle	Psoas
29	chr5:16884600-16887400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr5:16884800-16887400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:16884800-16887400	Enhancers	NHLF	lung
32	chr5:16885000-16887400	Enhancers	Placenta	Placenta
33	chr5:16885200-16889800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:16885200-16891000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:16885400-16887400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:16885400-16888200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:16885400-16894200	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:16885600-16888600	Weak transcription	Fetal Intestine Large	intestine
39	chr5:16885600-16888800	Weak transcription	HMEC	breast
40	chr5:16885600-16889000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr5:16885800-16887200	Enhancers	Fetal Muscle Trunk	muscle
42	chr5:16885800-16887400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr5:16885800-16887400	Enhancers	NH-A	brain
44	chr5:16885800-16887600	Enhancers	Adipose Nuclei	Adipose
45	chr5:16885800-16888600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr5:16886000-16887400	Enhancers	Left Ventricle	heart
47	chr5:16886000-16892400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr5:16886000-16893600	Weak transcription	Colonic Mucosa	Colon
49	chr5:16886200-16888200	Weak transcription	Gastric	stomach
50	chr5:16886200-16889600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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