Variant report

Variant	rs28380572
Chromosome Location	chr15:59639658-59639659
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10851653	0.85[ASN][1000 genomes]
rs11071432	0.85[ASN][1000 genomes]
rs11071433	0.85[ASN][1000 genomes]
rs11630796	0.90[ASN][1000 genomes]
rs11631146	0.84[ASN][1000 genomes]
rs11631451	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632346	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11635849	0.85[ASN][1000 genomes]
rs11637840	0.94[ASN][1000 genomes]
rs11639217	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11854697	0.94[ASN][1000 genomes]
rs11855765	0.88[ASN][1000 genomes]
rs11858264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11858313	0.97[ASN][1000 genomes]
rs12050546	0.88[ASN][1000 genomes]
rs12441388	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12442217	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12593355	0.97[ASN][1000 genomes]
rs12899138	0.85[ASN][1000 genomes]
rs12905793	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911676	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1580426	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16941369	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17236585	0.97[ASN][1000 genomes]
rs17302351	0.91[ASN][1000 genomes]
rs2170895	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28363891	0.97[ASN][1000 genomes]
rs28572451	0.97[ASN][1000 genomes]
rs4774327	0.88[ASN][1000 genomes]
rs4775158	0.85[ASN][1000 genomes]
rs59107240	0.99[ASN][1000 genomes]
rs61692274	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6494101	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494102	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494105	0.85[ASN][1000 genomes]
rs66595425	0.93[ASN][1000 genomes]
rs66991143	0.99[ASN][1000 genomes]
rs67498027	0.97[ASN][1000 genomes]
rs7162228	0.97[ASN][1000 genomes]
rs7168074	0.97[ASN][1000 genomes]
rs7173362	0.85[ASN][1000 genomes]
rs7178041	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8024396	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024879	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024906	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8025242	0.97[ASN][1000 genomes]
rs8025360	0.94[ASN][1000 genomes]
rs8031423	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8039327	0.97[ASN][1000 genomes]
rs8041804	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs965929	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv934082	chr15:59608605-59733211	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv457175	chr15:59609753-59681214	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv569603	chr15:59609753-59681214	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv471246	chr15:59610743-59681214	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv904274	chr15:59623576-59689378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59623200-59662800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:59623400-59641200	Weak transcription	Aorta	Aorta
3	chr15:59623400-59643800	Weak transcription	Lung	lung
4	chr15:59624600-59650000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:59626400-59641400	Weak transcription	HUVEC	blood vessel
6	chr15:59626400-59642400	Weak transcription	Pancreas	Pancrea
7	chr15:59631800-59641600	Weak transcription	HSMM	muscle
8	chr15:59631800-59641800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:59632000-59641600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:59632000-59641600	Weak transcription	NH-A	brain
11	chr15:59632000-59642200	Weak transcription	Left Ventricle	heart
12	chr15:59632000-59643600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:59632200-59641400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:59632600-59641400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:59632800-59640200	Weak transcription	HMEC	breast
16	chr15:59633000-59641200	Weak transcription	NHLF	lung
17	chr15:59634400-59641800	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:59634600-59640800	Genic enhancers	A549	lung
19	chr15:59634800-59662600	Weak transcription	Colonic Mucosa	Colon
20	chr15:59636400-59652800	Weak transcription	HepG2	liver
21	chr15:59636600-59643600	Weak transcription	Primary B cells from cord blood	blood
22	chr15:59636800-59640200	Weak transcription	Psoas Muscle	Psoas
23	chr15:59636800-59642000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:59636800-59642200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:59636800-59642200	Genic enhancers	Hela-S3	cervix
26	chr15:59636800-59642600	Weak transcription	Fetal Intestine Small	intestine
27	chr15:59637000-59641800	Weak transcription	Placenta	Placenta
28	chr15:59637000-59642400	Weak transcription	Spleen	Spleen
29	chr15:59637600-59640400	Genic enhancers	GM12878-XiMat	blood
30	chr15:59637600-59640600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:59637800-59641600	Weak transcription	NHDF-Ad	bronchial
32	chr15:59637800-59645200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:59637800-59662000	Weak transcription	Right Ventricle	heart
34	chr15:59638200-59639800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:59638200-59641400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:59638400-59639800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:59638400-59640200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:59638400-59641600	Weak transcription	Osteobl	bone
39	chr15:59638400-59642000	Weak transcription	Fetal Intestine Large	intestine
40	chr15:59638600-59640200	Weak transcription	NHEK	skin
41	chr15:59638600-59641600	Weak transcription	Adipose Nuclei	Adipose
42	chr15:59638600-59641600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr15:59638600-59641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:59638600-59642200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:59638600-59642400	Weak transcription	Fetal Heart	heart
46	chr15:59638600-59644200	Weak transcription	Brain Angular Gyrus	brain
47	chr15:59638600-59653000	Weak transcription	Esophagus	oesophagus
48	chr15:59638600-59654600	Weak transcription	Liver	Liver
49	chr15:59638800-59639800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:59639000-59640800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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