Variant report

Variant	rs13380185
Chromosome Location	chr15:56116563-56116564
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56090139..56092920-chr15:56116409..56118129,2	K562	blood:
2	chr15:56114839..56117156-chr15:56117660..56120029,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1042477	0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10851599	0.83[AFR][1000 genomes]
rs11071228	0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11630780	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11632977	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11633263	0.82[ASN][1000 genomes]
rs11633313	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12102014	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12102020	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12232351	0.81[ASN][1000 genomes]
rs12898589	0.95[ASN][1000 genomes]
rs12910830	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16976585	0.89[ASN][1000 genomes]
rs2288344	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2288345	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2414444	0.97[ASN][1000 genomes]
rs35040841	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56333939	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60890210	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162435	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7175686	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7176225	0.97[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs8024944	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8026172	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8028559	0.95[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	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13380185	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56095800-56128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:56106000-56131200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:56112200-56121800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:56112400-56124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:56112600-56119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:56112600-56122000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:56112600-56122000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:56112600-56122200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:56112600-56123800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:56112600-56133600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:56114400-56116800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:56114600-56128200	Weak transcription	Esophagus	oesophagus
13	chr15:56115200-56116600	Enhancers	Adipose Nuclei	Adipose
14	chr15:56115200-56116600	Enhancers	Osteobl	bone
15	chr15:56115200-56116800	Enhancers	Fetal Heart	heart
16	chr15:56115200-56116800	Enhancers	Rectal Smooth Muscle	rectum
17	chr15:56115400-56122400	Weak transcription	Aorta	Aorta
18	chr15:56115400-56148000	Weak transcription	Ovary	ovary
19	chr15:56115600-56116600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:56115600-56118600	Weak transcription	Brain Anterior Caudate	brain
21	chr15:56115600-56120000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:56115600-56121800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:56115800-56119400	Weak transcription	A549	lung
24	chr15:56115800-56119400	Weak transcription	HMEC	breast
25	chr15:56115800-56119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:56115800-56119800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:56115800-56120000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr15:56115800-56129800	Weak transcription	Hela-S3	cervix
29	chr15:56116000-56116600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:56116000-56116600	Enhancers	Stomach Smooth Muscle	stomach
31	chr15:56116000-56117200	Enhancers	Fetal Stomach	stomach
32	chr15:56116000-56120000	Weak transcription	Liver	Liver
33	chr15:56116000-56120200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:56116200-56116600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:56116200-56119400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:56116200-56120000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:56116200-56120000	Weak transcription	Psoas Muscle	Psoas
38	chr15:56116200-56120200	Weak transcription	NH-A	brain
39	chr15:56116200-56121800	Weak transcription	Fetal Muscle Leg	muscle
40	chr15:56116400-56116600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:56116400-56118000	Weak transcription	HSMM	muscle
42	chr15:56116400-56121800	Weak transcription	HSMMtube	muscle
43	chr15:56116400-56122200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:56116400-56122200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr15:56116400-56122400	Weak transcription	Fetal Intestine Small	intestine
46	chr15:56116400-56124800	Weak transcription	Colon Smooth Muscle	Colon
47	chr15:56116400-56129000	Weak transcription	NHLF	lung
48	chr15:56116400-56129600	Weak transcription	NHDF-Ad	bronchial
49	chr15:56116400-56133400	Weak transcription	Fetal Lung	lung

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