Variant report

Variant	rs28590577
Chromosome Location	chr15:78346106-78346107
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10519182	0.81[AFR][1000 genomes]
rs11629761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11634621	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11639164	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12102130	0.86[AFR][1000 genomes]
rs13329101	0.86[AFR][1000 genomes]
rs13329302	0.86[AFR][1000 genomes]
rs16969405	0.81[AFR][1000 genomes]
rs16969407	0.83[AFR][1000 genomes]
rs16969408	0.83[AFR][1000 genomes]
rs16969414	0.86[AFR][1000 genomes]
rs16969424	0.86[AFR][1000 genomes]
rs16969430	0.86[AFR][1000 genomes]
rs16969447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1985487	0.81[AFR][1000 genomes]
rs2044101	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28394000	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28417785	0.86[AFR][1000 genomes]
rs28441175	0.81[AFR][1000 genomes]
rs28451835	0.86[AFR][1000 genomes]
rs28485414	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28491820	0.86[AFR][1000 genomes]
rs28519575	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28526757	0.86[AFR][1000 genomes]
rs28591625	0.86[AFR][1000 genomes]
rs28593221	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28674965	0.81[AFR][1000 genomes]
rs55930913	0.83[AFR][1000 genomes]
rs58247186	0.94[AFR][1000 genomes]
rs74027705	0.81[AFR][1000 genomes]
rs74027706	0.81[AFR][1000 genomes]
rs74027709	0.81[AFR][1000 genomes]
rs9920647	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:78331400-78348600	Weak transcription	A549	lung
5	chr15:78331600-78348600	Weak transcription	K562	blood
6	chr15:78337000-78347800	Weak transcription	Ovary	ovary
7	chr15:78338800-78347000	Genic enhancers	Fetal Thymus	thymus
8	chr15:78339000-78346400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr15:78340800-78346200	Genic enhancers	Liver	Liver
10	chr15:78342600-78348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:78342800-78348600	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr15:78343000-78348400	Weak transcription	HMEC	breast
13	chr15:78343200-78346400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr15:78343200-78354200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:78343400-78348600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:78343600-78348400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:78343600-78348600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:78343800-78346400	Strong transcription	NHEK	skin
19	chr15:78343800-78347600	Weak transcription	Fetal Brain Male	brain
20	chr15:78343800-78347600	Weak transcription	Hela-S3	cervix
21	chr15:78343800-78348400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:78344000-78346200	Genic enhancers	HepG2	liver
23	chr15:78344000-78346600	Genic enhancers	Placenta	Placenta
24	chr15:78344400-78346200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:78344400-78346200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr15:78344400-78346200	Genic enhancers	Lung	lung
27	chr15:78344400-78346400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:78344400-78346400	Genic enhancers	Pancreas	Pancrea
29	chr15:78344400-78346400	Genic enhancers	Rectal Mucosa Donor 31	rectum
30	chr15:78344400-78346600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:78344400-78346800	Genic enhancers	HSMMtube	muscle
32	chr15:78344400-78352000	Genic enhancers	Fetal Intestine Small	intestine
33	chr15:78344600-78346400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:78344600-78346400	Genic enhancers	Primary monocytes fromperipheralblood	blood
35	chr15:78344600-78346400	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr15:78344600-78346400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:78344600-78346600	Genic enhancers	Dnd41	blood
38	chr15:78344600-78348000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr15:78344800-78346200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:78344800-78346400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:78344800-78346400	Genic enhancers	Brain Hippocampus Middle	brain
42	chr15:78344800-78346400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr15:78344800-78346400	Genic enhancers	Thymus	Thymus
44	chr15:78344800-78346600	Genic enhancers	GM12878-XiMat	blood
45	chr15:78344800-78347000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:78344800-78347400	Weak transcription	Psoas Muscle	Psoas
47	chr15:78344800-78348200	Weak transcription	Right Ventricle	heart
48	chr15:78344800-78348600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr15:78344800-78348600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr15:78344800-78348800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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