Variant report

Variant	rs58185101
Chromosome Location	chr15:52857616-52857617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52547521..52550331-chr15:52856320..52858197,2	MCF-7	breast:
2	chr15:52856629..52859409-chr15:52967140..52969725,2	K562	blood:
3	chr15:52548177..52549010-chr15:52857432..52858401,2	MCF-7	breast:
4	chr15:52856310..52859319-chr15:52859336..52861902,3	K562	blood:
5	chr15:52856954..52860622-chr15:52999914..53003074,3	MCF-7	breast:
6	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:
7	chr15:52640299..52642947-chr15:52856133..52857726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1055746	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1055747	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11539782	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11852533	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11853096	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11853137	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11854942	0.80[AMR][1000 genomes]
rs11854997	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11855859	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857682	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858238	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542396	0.89[AMR][1000 genomes]
rs17542520	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17542527	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17614428	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17614498	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614529	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049517	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049518	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2899490	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3478	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774633	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4776055	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4776056	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55800146	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56947153	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.87[AMR][1000 genomes]
rs58246435	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60426742	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396714	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396718	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73396723	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396728	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396733	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74014300	0.85[AMR][1000 genomes]
rs74016845	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS 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	51 gene(s)	inside rSNPs	diseases
3	esv1832020	chr15:52702400-52901914	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1047775	chr15:52822050-52912228	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs58185101	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs58185101	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs58185101	ARPP19	cis	Adipose Subcutaneous	GTEx
rs58185101	ARPP19	cis	Artery Tibial	GTEx
rs58185101	ARPP19	cis	Whole Blood	GTEx
rs58185101	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs58185101	ARPP19	cis	Thyroid	GTEx
rs58185101	ARPP19	cis	Esophagus Muscularis	GTEx
rs58185101	ARPP19	cis	Muscle Skeletal	GTEx
rs58185101	ARPP19	cis	Nerve Tibial	GTEx
rs58185101	ARPP19	cis	Heart Left Ventricle	GTEx
rs58185101	ARPP19	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
5	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
6	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
7	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:52844600-52859000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:52846200-52859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:52847000-52859400	Weak transcription	Fetal Intestine Large	intestine
13	chr15:52849400-52859000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:52849400-52860000	Weak transcription	Placenta	Placenta
15	chr15:52850000-52859200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:52850200-52858200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr15:52850200-52859200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr15:52850800-52859000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:52850800-52859000	Weak transcription	HSMMtube	muscle
20	chr15:52851600-52859200	Weak transcription	Fetal Kidney	kidney
21	chr15:52851600-52859200	Weak transcription	HSMM	muscle
22	chr15:52852000-52858200	Weak transcription	Spleen	Spleen
23	chr15:52852200-52858400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:52852200-52858800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:52852200-52858800	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:52852200-52859000	Weak transcription	Fetal Intestine Small	intestine
27	chr15:52853000-52859000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52853200-52859200	Weak transcription	Fetal Brain Female	brain
29	chr15:52853200-52860000	Weak transcription	Gastric	stomach
30	chr15:52853400-52858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:52853400-52859000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:52853400-52859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr15:52853400-52859200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:52853400-52859200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:52853600-52859000	Weak transcription	NHLF	lung
36	chr15:52853800-52859000	Weak transcription	Fetal Heart	heart
37	chr15:52854000-52859600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr15:52854600-52859000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:52854600-52859400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr15:52854800-52859000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:52854800-52860000	Enhancers	Primary T cells fromperipheralblood	blood
42	chr15:52855200-52858000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:52855200-52860200	Enhancers	Small Intestine	intestine
44	chr15:52855800-52857800	Enhancers	Brain Hippocampus Middle	brain
45	chr15:52855800-52857800	Enhancers	Rectal Smooth Muscle	rectum
46	chr15:52855800-52858000	Enhancers	Brain Anterior Caudate	brain
47	chr15:52855800-52858000	Enhancers	Colon Smooth Muscle	Colon
48	chr15:52855800-52858000	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr15:52855800-52858000	Genic enhancers	A549	lung
50	chr15:52856000-52858000	Enhancers	Duodenum Smooth Muscle	Duodenum

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