Variant report

Variant	rs7179116
Chromosome Location	chr15:56174827-56174828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1042477	0.87[ASW][hapmap];0.85[MKK][hapmap]
rs10851599	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071228	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11071231	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632096	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632295	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11633263	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633313	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636123	0.90[EUR][1000 genomes]
rs11637576	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12102014	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12102020	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12232351	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595359	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12595728	0.83[EUR][1000 genomes]
rs1509406	0.92[CEU][hapmap];0.89[CHB][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16976600	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1912398	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1912402	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2089635	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2089636	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2102465	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2288344	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28660477	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28770330	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28773028	0.85[EUR][1000 genomes]
rs28778631	0.90[EUR][1000 genomes]
rs28825119	0.83[EUR][1000 genomes]
rs28863270	0.89[EUR][1000 genomes]
rs56333939	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60482539	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66462353	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67505007	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162435	0.96[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7175686	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176225	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7182397	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72732282	0.85[EUR][1000 genomes]
rs72734373	0.85[EUR][1000 genomes]
rs8024944	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8026172	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8029247	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs8032158	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8038646	0.85[EUR][1000 genomes]
rs8038884	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9920158	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9920159	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9920184	0.80[AMR][1000 genomes];0.87[EUR][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	esv2761966	chr15:56167250-56192861	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3361699	chr15:56173709-56192307	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7179116	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56149000-56177600	Weak transcription	Spleen	Spleen
2	chr15:56153000-56176400	Weak transcription	Esophagus	oesophagus
3	chr15:56153600-56178600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:56155400-56175600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:56158200-56176400	Weak transcription	Left Ventricle	heart
6	chr15:56161200-56179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:56161400-56177400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:56166000-56185400	Weak transcription	Hela-S3	cervix
9	chr15:56167800-56176200	Weak transcription	Psoas Muscle	Psoas
10	chr15:56171400-56177600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:56171600-56175600	Weak transcription	Aorta	Aorta
12	chr15:56171800-56176400	Weak transcription	HUVEC	blood vessel
13	chr15:56172000-56177200	Weak transcription	Fetal Stomach	stomach
14	chr15:56172000-56177600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:56172000-56186200	Weak transcription	Osteobl	bone
16	chr15:56172800-56176400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:56172800-56176800	Weak transcription	Pancreas	Pancrea
18	chr15:56172800-56189600	Weak transcription	Placenta	Placenta
19	chr15:56173200-56175600	Weak transcription	Right Ventricle	heart
20	chr15:56174000-56175600	Genic enhancers	A549	lung
21	chr15:56174200-56175000	Strong transcription	Liver	Liver
22	chr15:56174200-56177400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:56174400-56175000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:56174400-56175000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:56174400-56175000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr15:56174400-56175200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr15:56174400-56175600	Strong transcription	HSMMtube	muscle
28	chr15:56174400-56175600	Strong transcription	NHEK	skin
29	chr15:56174400-56175800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:56174400-56175800	Strong transcription	HSMM	muscle
31	chr15:56174400-56177800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:56174600-56175400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:56174600-56175400	Strong transcription	Primary T cells from cord blood	blood
34	chr15:56174600-56175400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:56174600-56175600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:56174600-56175800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:56174600-56176000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr15:56174600-56181000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:56174800-56175200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:56174800-56175200	Weak transcription	Lung	lung
41	chr15:56174800-56175400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr15:56174800-56176000	Strong transcription	Fetal Intestine Small	intestine
43	chr15:56174800-56177400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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