Variant report

Variant	rs28609562
Chromosome Location	chr5:75997678-75997679
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10036196	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10036832	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10053089	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10055683	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10056941	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058007	0.84[ASN][1000 genomes]
rs10062454	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10063755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10063791	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10063832	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078999	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10213750	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10213957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214134	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474484	0.84[ASN][1000 genomes]
rs10942789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942790	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942791	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11950408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11951708	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951902	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11952627	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11953613	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11956898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054930	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517193	0.84[ASN][1000 genomes]
rs12697858	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13154881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13154915	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13168057	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175585	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13181615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188539	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13188565	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13188750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227744	0.84[ASN][1000 genomes]
rs2307122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2307123	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2307124	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34921325	0.84[ASN][1000 genomes]
rs3797451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822547	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822548	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703715	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4703716	0.84[ASN][1000 genomes]
rs4704354	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704355	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704356	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4704357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71630933	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7712485	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7731047	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9293695	0.84[ASN][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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882207	chr5:75997213-76027823	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882208	chr5:75997213-76034355	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75945200-76001000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr5:75946400-76001000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:75948000-76004600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:75950800-75999400	Weak transcription	Ovary	ovary
5	chr5:75951800-76001400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:75969800-75999600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:75975600-75999600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:75977600-76003400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:75978400-76001600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr5:75978400-76004400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:75978600-76003400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr5:75980600-76002600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:75980800-76000200	Strong transcription	Primary hematopoietic stem cells	blood
14	chr5:75981200-76001600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:75985800-76004400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:75986600-76000000	Strong transcription	Primary B cells from cord blood	blood
17	chr5:75987600-76001200	Weak transcription	Small Intestine	intestine
18	chr5:75987800-76001400	Weak transcription	Fetal Lung	lung
19	chr5:75988000-75999200	Weak transcription	Stomach Mucosa	stomach
20	chr5:75988200-75999400	Strong transcription	Placenta	Placenta
21	chr5:75988200-75999600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:75988400-75998600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:75988400-76004600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:75988600-76001800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:75988600-76007800	Weak transcription	Fetal Intestine Large	intestine
26	chr5:75988800-75999000	Weak transcription	Fetal Kidney	kidney
27	chr5:75988800-76006600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:75988800-76011000	Weak transcription	Lung	lung
29	chr5:75989000-75997800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr5:75989200-76000000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:75989600-76010400	Weak transcription	Fetal Intestine Small	intestine
32	chr5:75990600-75999600	Weak transcription	Adipose Nuclei	Adipose
33	chr5:75990800-75999600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:75991000-76000800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:75991400-76010600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:75991600-76005800	Weak transcription	Fetal Muscle Leg	muscle
37	chr5:75992800-76000400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:75993000-75999600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:75993000-76000200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:75993000-76000400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:75993200-75998400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr5:75993200-76000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:75993400-76001400	Strong transcription	Primary T cells from cord blood	blood
44	chr5:75993800-76001600	Weak transcription	K562	blood
45	chr5:75993800-76004200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:75994200-76006400	Weak transcription	GM12878-XiMat	blood
47	chr5:75994400-75998800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr5:75994400-75999800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:75995800-76004000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:75996000-75997800	Strong transcription	Pancreas	Pancrea

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