Variant report

Variant	rs28863270
Chromosome Location	chr15:56250029-56250030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56249710..56252114-chr15:56284678..56286584,2	MCF-7	breast:
2	chr15:56249277..56251562-chr15:56285197..56286697,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069869	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10851599	0.83[EUR][1000 genomes]
rs11071231	0.82[EUR][1000 genomes]
rs11071234	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632096	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11632295	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636123	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11637576	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595359	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595728	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509406	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16976600	0.83[EUR][1000 genomes]
rs1912398	0.82[EUR][1000 genomes]
rs1912402	0.82[EUR][1000 genomes]
rs2089635	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2089636	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2102465	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28660477	0.82[EUR][1000 genomes]
rs28770330	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28773028	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28778631	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28825119	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59912282	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60482539	0.91[EUR][1000 genomes]
rs66462353	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67505007	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7179116	0.89[EUR][1000 genomes]
rs7182397	0.91[EUR][1000 genomes]
rs72734373	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029247	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8032158	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8038646	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038884	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920158	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920159	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920184	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28863270	PRTG	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56229400-56259000	Weak transcription	Ovary	ovary
2	chr15:56229400-56259400	Weak transcription	Small Intestine	intestine
3	chr15:56229600-56251600	Weak transcription	K562	blood
4	chr15:56229600-56282600	Weak transcription	NHLF	lung
5	chr15:56229800-56259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:56231600-56260000	Weak transcription	Left Ventricle	heart
8	chr15:56232200-56251600	Weak transcription	HSMMtube	muscle
9	chr15:56232600-56257200	Weak transcription	Primary T cells from cord blood	blood
10	chr15:56235800-56253600	Weak transcription	Fetal Lung	lung
11	chr15:56236000-56258200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:56236000-56259000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:56236000-56261200	Weak transcription	Esophagus	oesophagus
14	chr15:56236200-56257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:56236200-56257000	Weak transcription	Aorta	Aorta
16	chr15:56236200-56276000	Weak transcription	HUVEC	blood vessel
17	chr15:56236600-56257000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:56236800-56251600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:56236800-56257000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:56236800-56282800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:56237000-56251800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:56238200-56257000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:56241000-56261400	Weak transcription	Pancreas	Pancrea
24	chr15:56242800-56255600	Weak transcription	Hela-S3	cervix
25	chr15:56243000-56257000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:56243200-56250400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:56243200-56251400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:56243200-56253200	Weak transcription	NHEK	skin
29	chr15:56243200-56253400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:56243200-56255600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:56243200-56256400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:56243200-56256400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr15:56243200-56276200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr15:56243400-56253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:56243400-56253000	Weak transcription	HMEC	breast
36	chr15:56243400-56253200	Weak transcription	HSMM	muscle
37	chr15:56243400-56257000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:56244600-56257800	Weak transcription	Fetal Brain Male	brain
39	chr15:56247400-56253000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:56247400-56257000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:56247600-56251200	Weak transcription	Fetal Intestine Large	intestine
42	chr15:56247600-56251800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr15:56247600-56252000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:56247600-56253000	Weak transcription	Gastric	stomach
45	chr15:56247600-56257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:56247800-56254800	Weak transcription	Fetal Intestine Small	intestine
47	chr15:56248000-56250600	Weak transcription	A549	lung
48	chr15:56248200-56285200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:56248800-56251200	Weak transcription	HepG2	liver
50	chr15:56250000-56266600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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