Variant report

Variant	rs58246435
Chromosome Location	chr15:52859572-52859573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52859559..52861665-chr2:55842687..55845255,2	MCF-7	breast:
2	chr15:50646435..50649191-chr15:52859384..52862079,2	MCF-7	breast:
3	chr15:52820217..52824623-chr15:52859000..52863588,7	MCF-7	breast:
4	chr15:52121756..52123415-chr15:52859545..52862503,2	MCF-7	breast:
5	chr15:52858243..52860799-chr15:52942874..52945480,2	K562	blood:
6	chr15:52585776..52589284-chr15:52859101..52864638,8	MCF-7	breast:
7	chr15:52856954..52860622-chr15:52999914..53003074,3	MCF-7	breast:
8	chr15:52857884..52859774-chr20:53285881..53288351,2	MCF-7	breast:
9	chr15:52585351..52588570-chr15:52858851..52862304,3	MCF-7	breast:
10	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000197535	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000272606	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1055746	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1055747	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11539782	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852533	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11853096	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11853137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11854997	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11855859	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11857682	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11858238	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542396	0.86[AMR][1000 genomes]
rs17542520	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17542527	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17614428	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17614498	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17614529	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049517	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049518	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2899490	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3478	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4774633	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776055	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776056	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55800146	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56947153	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.84[AMR][1000 genomes]
rs58185101	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60426742	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73396714	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73396718	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73396723	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396728	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396733	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74014300	0.82[AMR][1000 genomes]
rs74016845	0.98[AMR][1000 genomes];0.97[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs58246435	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs58246435	ARPP19	cis	Whole Blood	GTEx
rs58246435	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs58246435	ARPP19	cis	Artery Tibial	GTEx
rs58246435	ARPP19	cis	Esophagus Muscularis	GTEx
rs58246435	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs58246435	ARPP19	cis	Nerve Tibial	GTEx
rs58246435	ARPP19	cis	Heart Left Ventricle	GTEx
rs58246435	ARPP19	cis	Artery Aorta	GTEx
rs58246435	ARPP19	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 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	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
4	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:52849400-52860000	Weak transcription	Placenta	Placenta
7	chr15:52853200-52860000	Weak transcription	Gastric	stomach
8	chr15:52854000-52859600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:52854800-52860000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr15:52855200-52860200	Enhancers	Small Intestine	intestine
11	chr15:52857000-52860000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:52857200-52860000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr15:52857200-52860000	Enhancers	Primary B cells from peripheral blood	blood
14	chr15:52857400-52860000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr15:52857600-52860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:52858200-52860000	Enhancers	Left Ventricle	heart
17	chr15:52858200-52860000	Weak transcription	Lung	lung
18	chr15:52858600-52861800	Active TSS	GM12878-XiMat	blood
19	chr15:52858800-52859600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:52858800-52859600	Enhancers	Fetal Muscle Leg	muscle
21	chr15:52858800-52859800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr15:52858800-52860000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:52858800-52860200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:52858800-52860400	Enhancers	Spleen	Spleen
25	chr15:52858800-52861000	Active TSS	Right Atrium	heart
26	chr15:52858800-52861400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr15:52858800-52861600	Active TSS	Psoas Muscle	Psoas
28	chr15:52858800-52861800	Active TSS	HMEC	breast
29	chr15:52859000-52859600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:52859000-52859600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr15:52859000-52859600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:52859000-52859600	Enhancers	Fetal Brain Male	brain
33	chr15:52859000-52859600	Flanking Active TSS	Hela-S3	cervix
34	chr15:52859000-52859600	Flanking Active TSS	HepG2	liver
35	chr15:52859000-52859800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr15:52859000-52859800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr15:52859000-52859800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
38	chr15:52859000-52859800	Flanking Active TSS	NHEK	skin
39	chr15:52859000-52860000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:52859000-52860000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:52859000-52860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:52859000-52860000	Flanking Active TSS	Dnd41	blood
43	chr15:52859000-52860000	Flanking Active TSS	HUVEC	blood vessel
44	chr15:52859000-52860200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:52859000-52860200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr15:52859000-52860200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:52859000-52860200	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr15:52859000-52860400	Flanking Active TSS	Liver	Liver
49	chr15:52859000-52860400	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr15:52859000-52860600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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