Variant report

Variant	rs1912398
Chromosome Location	chr15:56159103-56159104
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851599	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11071228	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11071231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632096	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11632295	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633263	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11633313	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11636123	0.83[EUR][1000 genomes]
rs11637576	0.82[EUR][1000 genomes]
rs12102014	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12102020	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12232351	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12595359	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1509406	0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs16976600	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2089635	0.81[EUR][1000 genomes]
rs2089636	0.81[EUR][1000 genomes]
rs2288344	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28660477	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28770330	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28778631	0.83[EUR][1000 genomes]
rs28863270	0.82[EUR][1000 genomes]
rs56333939	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60482539	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66462353	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67505007	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7162435	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7175686	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7176225	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7179116	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7182397	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72732282	0.86[EUR][1000 genomes]
rs8024944	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8026172	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8028559	0.81[EUR][1000 genomes]
rs8029247	0.85[CHB][hapmap]
rs8032158	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8038884	0.83[EUR][1000 genomes]
rs9920158	0.80[AMR][1000 genomes]
rs9920159	0.80[AMR][1000 genomes];0.81[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1912398	PRTG	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
2	chr15:56132000-56164800	Weak transcription	Small Intestine	intestine
3	chr15:56138200-56161800	Weak transcription	K562	blood
4	chr15:56148000-56160400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:56148200-56174400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:56148800-56161800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:56149000-56163600	Weak transcription	Gastric	stomach
8	chr15:56149000-56164800	Weak transcription	Aorta	Aorta
9	chr15:56149000-56177600	Weak transcription	Spleen	Spleen
10	chr15:56152400-56164800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:56152800-56165000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:56152800-56174600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:56153000-56160400	Weak transcription	Primary T cells from cord blood	blood
14	chr15:56153000-56161000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:56153000-56161000	Weak transcription	HepG2	liver
16	chr15:56153000-56163200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:56153000-56163800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:56153000-56164800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:56153000-56164800	Weak transcription	Ovary	ovary
20	chr15:56153000-56167400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:56153000-56174000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:56153000-56174400	Weak transcription	HSMMtube	muscle
23	chr15:56153000-56174800	Weak transcription	Fetal Intestine Small	intestine
24	chr15:56153000-56176400	Weak transcription	Esophagus	oesophagus
25	chr15:56153200-56161000	Weak transcription	Hela-S3	cervix
26	chr15:56153600-56178600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:56153800-56161000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:56153800-56161000	Weak transcription	HUVEC	blood vessel
29	chr15:56153800-56165600	Weak transcription	HMEC	breast
30	chr15:56154000-56160600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:56154200-56160400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:56154400-56160400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr15:56154400-56162600	Weak transcription	NHDF-Ad	bronchial
34	chr15:56154400-56164800	Weak transcription	Psoas Muscle	Psoas
35	chr15:56154400-56164800	Weak transcription	NH-A	brain
36	chr15:56154800-56160400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:56154800-56161000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:56155000-56160200	Weak transcription	NHEK	skin
39	chr15:56155000-56160600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:56155400-56160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:56155400-56160600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:56155400-56161000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:56155400-56165200	Weak transcription	Fetal Intestine Large	intestine
44	chr15:56155400-56174800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr15:56155400-56175600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:56155600-56160400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:56155600-56161000	Weak transcription	Liver	Liver
48	chr15:56155600-56161200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:56156200-56165600	Strong transcription	HSMM	muscle
50	chr15:56158200-56160400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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