Variant report

Variant	rs73396733
Chromosome Location	chr15:52859669-52859670
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 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	chr15:52859630..52861792-chr2:21021008..21023718,2	MCF-7	breast:
10	chr15:52585351..52588570-chr15:52858851..52862304,3	MCF-7	breast:
11	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000138594	Chromatin interaction
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000118961	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1055746	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1055747	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11539782	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11852533	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11853096	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11853137	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11854942	0.84[AMR][1000 genomes]
rs11854997	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11855859	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857682	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11858238	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17542396	0.93[AMR][1000 genomes]
rs17542520	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17542527	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17614428	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17614498	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614529	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049517	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049518	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2899490	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3478	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774633	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4776055	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4776056	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55800146	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56947153	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.91[AMR][1000 genomes]
rs58185101	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58246435	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60426742	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396714	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396718	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73396723	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396728	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74014300	0.89[AMR][1000 genomes]
rs74016845	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs73396733	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs73396733	ARPP19	cis	Nerve Tibial	GTEx
rs73396733	ARPP19	cis	Adipose Subcutaneous	GTEx
rs73396733	ARPP19	cis	Whole Blood	GTEx
rs73396733	ARPP19	cis	Artery Tibial	GTEx
rs73396733	ARPP19	cis	Heart Left Ventricle	GTEx
rs73396733	ARPP19	cis	Esophagus Muscularis	GTEx
rs73396733	ARPP19	cis	Thyroid	GTEx
rs73396733	ARPP19	cis	lung	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	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:52849400-52860000	Weak transcription	Placenta	Placenta
6	chr15:52853200-52860000	Weak transcription	Gastric	stomach
7	chr15:52854800-52860000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr15:52855200-52860200	Enhancers	Small Intestine	intestine
9	chr15:52857000-52860000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:52857200-52860000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr15:52857200-52860000	Enhancers	Primary B cells from peripheral blood	blood
12	chr15:52857400-52860000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr15:52857600-52860000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:52858200-52860000	Enhancers	Left Ventricle	heart
15	chr15:52858200-52860000	Weak transcription	Lung	lung
16	chr15:52858600-52861800	Active TSS	GM12878-XiMat	blood
17	chr15:52858800-52859800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr15:52858800-52860000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:52858800-52860200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr15:52858800-52860400	Enhancers	Spleen	Spleen
21	chr15:52858800-52861000	Active TSS	Right Atrium	heart
22	chr15:52858800-52861400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr15:52858800-52861600	Active TSS	Psoas Muscle	Psoas
24	chr15:52858800-52861800	Active TSS	HMEC	breast
25	chr15:52859000-52859800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr15:52859000-52859800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr15:52859000-52859800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
28	chr15:52859000-52859800	Flanking Active TSS	NHEK	skin
29	chr15:52859000-52860000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:52859000-52860000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:52859000-52860000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr15:52859000-52860000	Flanking Active TSS	Dnd41	blood
33	chr15:52859000-52860000	Flanking Active TSS	HUVEC	blood vessel
34	chr15:52859000-52860200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:52859000-52860200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr15:52859000-52860200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:52859000-52860200	Flanking Active TSS	Rectal Smooth Muscle	rectum
38	chr15:52859000-52860400	Flanking Active TSS	Liver	Liver
39	chr15:52859000-52860400	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr15:52859000-52860600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52859000-52860800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:52859000-52860800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr15:52859000-52861000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:52859000-52861200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:52859000-52861400	Active TSS	H1 Cell Line	embryonic stem cell
46	chr15:52859000-52861400	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr15:52859000-52861400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr15:52859000-52861400	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:52859000-52861400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr15:52859000-52861600	Active TSS	NHLF	lung

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