Variant report

Variant	rs2102465
Chromosome Location	chr15:56252609-56252610
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	chr15:56251937..56254023-chr15:56256235..56258687,3	K562	blood:
2	chr15:56250089..56252612-chr15:56259045..56261387,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10851599	0.80[EUR][1000 genomes]
rs11071234	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632096	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11632295	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636123	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637576	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595359	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12595728	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1509406	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16976600	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2089635	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2089636	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28660477	0.80[AMR][1000 genomes]
rs28770330	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28773028	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28778631	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28825119	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28863270	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59912282	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60482539	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66462353	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67505007	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7179116	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182397	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72734373	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8029247	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8032158	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8038646	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8038884	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920158	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920159	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920184	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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
rs2102465	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

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	chr15:56229600-56282600	Weak transcription	NHLF	lung
4	chr15:56229800-56259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:56231600-56260000	Weak transcription	Left Ventricle	heart
7	chr15:56232600-56257200	Weak transcription	Primary T cells from cord blood	blood
8	chr15:56235800-56253600	Weak transcription	Fetal Lung	lung
9	chr15:56236000-56258200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:56236000-56259000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr15:56236000-56261200	Weak transcription	Esophagus	oesophagus
12	chr15:56236200-56257000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:56236200-56257000	Weak transcription	Aorta	Aorta
14	chr15:56236200-56276000	Weak transcription	HUVEC	blood vessel
15	chr15:56236600-56257000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:56236800-56257000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:56236800-56282800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:56238200-56257000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:56241000-56261400	Weak transcription	Pancreas	Pancrea
20	chr15:56242800-56255600	Weak transcription	Hela-S3	cervix
21	chr15:56243000-56257000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:56243200-56253200	Weak transcription	NHEK	skin
23	chr15:56243200-56253400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:56243200-56255600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:56243200-56256400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:56243200-56256400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:56243200-56276200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:56243400-56253000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:56243400-56253000	Weak transcription	HMEC	breast
30	chr15:56243400-56253200	Weak transcription	HSMM	muscle
31	chr15:56243400-56257000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:56244600-56257800	Weak transcription	Fetal Brain Male	brain
33	chr15:56247400-56253000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:56247400-56257000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:56247600-56253000	Weak transcription	Gastric	stomach
36	chr15:56247600-56257400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:56247800-56254800	Weak transcription	Fetal Intestine Small	intestine
38	chr15:56248200-56285200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:56250000-56266600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:56250600-56253000	Weak transcription	Lung	lung
41	chr15:56250600-56257200	Weak transcription	Fetal Stomach	stomach
42	chr15:56251200-56253600	Enhancers	Fetal Intestine Large	intestine
43	chr15:56251200-56253600	Enhancers	HepG2	liver
44	chr15:56251200-56258200	Weak transcription	A549	lung
45	chr15:56251600-56253200	Enhancers	HSMMtube	muscle
46	chr15:56251600-56253400	Enhancers	K562	blood
47	chr15:56251600-56281600	Weak transcription	Osteobl	bone
48	chr15:56251800-56253400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:56252000-56253400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr15:56252200-56253000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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