Variant report

Variant	rs2089635
Chromosome Location	chr15:56236588-56236589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10851599	0.81[EUR][1000 genomes]
rs11071231	0.81[EUR][1000 genomes]
rs11071234	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632096	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632295	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636123	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637576	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595359	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12595728	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1509406	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16976600	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1912398	0.81[EUR][1000 genomes]
rs1912402	0.81[EUR][1000 genomes]
rs2089636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102465	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28660477	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28770330	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28773028	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28778631	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28825119	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28863270	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59912282	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60482539	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66462353	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs67505007	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7179116	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7182397	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72734373	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029247	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032158	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8038646	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8038884	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920158	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920159	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920184	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs2089635	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56209600-56247400	Weak transcription	Psoas Muscle	Psoas
2	chr15:56211800-56242400	Weak transcription	Hela-S3	cervix
3	chr15:56221600-56242400	Weak transcription	NHEK	skin
4	chr15:56226200-56245800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:56229400-56259000	Weak transcription	Ovary	ovary
6	chr15:56229400-56259400	Weak transcription	Small Intestine	intestine
7	chr15:56229600-56251600	Weak transcription	K562	blood
8	chr15:56229600-56282600	Weak transcription	NHLF	lung
9	chr15:56229800-56242600	Weak transcription	Osteobl	bone
10	chr15:56229800-56259000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:56230200-56237000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:56230400-56242600	Weak transcription	HSMM	muscle
13	chr15:56230800-56242400	Weak transcription	A549	lung
14	chr15:56231000-56244600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:56231600-56260000	Weak transcription	Left Ventricle	heart
17	chr15:56232200-56251600	Weak transcription	HSMMtube	muscle
18	chr15:56232600-56238200	Weak transcription	Thymus	Thymus
19	chr15:56232600-56257200	Weak transcription	Primary T cells from cord blood	blood
20	chr15:56233400-56242600	Weak transcription	HMEC	breast
21	chr15:56233800-56236800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:56234000-56236600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:56234000-56236800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:56234000-56237000	Strong transcription	Fetal Intestine Large	intestine
25	chr15:56234200-56236600	Strong transcription	Liver	Liver
26	chr15:56234600-56236800	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr15:56234800-56237000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr15:56234800-56238200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr15:56234800-56238200	Weak transcription	Placenta	Placenta
30	chr15:56235200-56236600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:56235200-56236800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:56235200-56236800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:56235200-56239800	Weak transcription	Gastric	stomach
34	chr15:56235200-56242800	Weak transcription	Adipose Nuclei	Adipose
35	chr15:56235400-56236600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr15:56235400-56236800	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr15:56235400-56236800	ZNF genes & repeats	Fetal Stomach	stomach
38	chr15:56235400-56238800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:56235600-56236600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:56235600-56236600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:56235600-56238600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr15:56235800-56236600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:56235800-56237400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr15:56235800-56253600	Weak transcription	Fetal Lung	lung
45	chr15:56236000-56236600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:56236000-56237600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:56236000-56242200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:56236000-56246000	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:56236000-56258200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:56236000-56259000	Weak transcription	Fetal Muscle Trunk	muscle

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