Variant report

Variant	rs17614529
Chromosome Location	chr15:52850352-52850353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52850326-52850536	A549	lung:	n/a	n/a
2	BCL3	chr15:52850322-52850788	GM12878	blood:	n/a	n/a
3	NFIC	chr15:52850262-52850945	GM12878	blood:	n/a	n/a
4	BCL11A	chr15:52850301-52850697	GM12878	blood:	n/a	n/a
5	ATF2	chr15:52850315-52850838	GM12878	blood:	n/a	n/a
6	YY1	chr15:52850304-52850643	GM12892	blood:	n/a	n/a
7	BATF	chr15:52850334-52850858	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:52850143-52850842	GM12892	blood:	n/a	n/a
9	CHD1	chr15:52850175-52850819	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:52850338-52850770	MCF10A-Er-Src	breast:	n/a	n/a
11	BCLAF1	chr15:52850248-52850922	GM12878	blood:	n/a	n/a
12	EBF1	chr15:52850295-52850738	GM12878	blood:	n/a	n/a
13	CREB1	chr15:52850279-52850872	GM12878	blood:	n/a	n/a
14	POLR2A	chr15:52850266-52850643	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr15:52850060-52850876	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:52850176-52850773	GM12892	blood:	n/a	n/a
17	YY1	chr15:52850343-52850763	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:52850339-52850661	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:52850192-52850839	GM12878	blood:	n/a	n/a
20	RUNX3	chr15:52850241-52850753	GM12878	blood:	n/a	n/a
21	WRNIP1	chr15:52850314-52850664	GM12878	blood:	n/a	n/a
22	STAT3	chr15:52850243-52850829	GM12878	blood:	n/a	n/a
23	FOXM1	chr15:52850253-52850855	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:52850178-52850813	GM12892	blood:	n/a	n/a
25	PAX5	chr15:52850316-52850688	GM12878	blood:	n/a	n/a
26	YY1	chr15:52850327-52850674	GM12878	blood:	n/a	n/a
27	REST	chr15:52850211-52850835	MCF-7	breast:	n/a	n/a
28	IKZF1	chr15:52850262-52850896	GM12878	blood:	n/a	n/a
29	POU2F2	chr15:52850303-52850757	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:52850292-52850636	K562	blood:	n/a	n/a
31	YY1	chr15:52850293-52850659	K562	blood:	n/a	n/a
32	ZNF384	chr15:52850293-52851291	GM12878	blood:	n/a	n/a
33	TAF1	chr15:52850303-52850698	GM12878	blood:	n/a	n/a
34	RUNX3	chr15:52850248-52850887	GM12878	blood:	n/a	n/a
35	ATF2	chr15:52850236-52850920	GM12878	blood:	n/a	n/a
36	POLR2A	chr15:52850272-52850665	GM12891	blood:	n/a	n/a
37	POLR2A	chr15:52850031-52850807	HepG2	liver:	n/a	n/a

No data

Variant related genes	Relation type
ARPP19	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1055746	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1055747	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11539782	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11852533	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11853096	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11853137	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11854942	0.82[AMR][1000 genomes]
rs11854997	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11855859	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11857682	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11858238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858875	0.86[CEU][hapmap]
rs17542396	0.91[AMR][1000 genomes]
rs17542520	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17542527	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17614428	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17614498	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2049517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049518	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2899490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3478	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4774633	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776055	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4776056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55800146	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56947153	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.89[AMR][1000 genomes]
rs58185101	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58246435	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60426742	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73396714	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73396718	0.93[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	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74014300	0.87[AMR][1000 genomes]
rs74016845	0.84[AMR][1000 genomes];0.93[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
rs17614529	ARPP19	cis	Whole Blood	GTEx
rs17614529	ARPP19	cis	Adipose Subcutaneous	GTEx
rs17614529	ARPP19	cis	lung	GTEx
rs17614529	ARPP19	cis	Thyroid	GTEx
rs17614529	ARPP19	cis	Esophagus Muscularis	GTEx
rs17614529	ARPP19	cis	Heart Left Ventricle	GTEx
rs17614529	ARPP19	cis	Nerve Tibial	GTEx
rs17614529	ARPP19	cis	Artery Tibial	GTEx
rs17614529	ARPP19	cis	Muscle Skeletal	GTEx
rs17614529	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs17614529	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs17614529	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
2	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
3	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
4	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:52838000-52853000	Strong transcription	Dnd41	blood
7	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:52839000-52851400	Weak transcription	Gastric	stomach
10	chr15:52839000-52851400	Weak transcription	Spleen	Spleen
11	chr15:52839000-52853400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
14	chr15:52839200-52851000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:52839200-52851000	Weak transcription	Esophagus	oesophagus
16	chr15:52839200-52851800	Weak transcription	Right Ventricle	heart
17	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
18	chr15:52841000-52857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:52841200-52850400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
21	chr15:52842800-52851400	Weak transcription	Fetal Heart	heart
22	chr15:52843600-52852600	Weak transcription	Brain Substantia Nigra	brain
23	chr15:52844200-52850400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr15:52844200-52851000	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:52844200-52852800	Weak transcription	Fetal Brain Female	brain
26	chr15:52844400-52855200	Weak transcription	Fetal Lung	lung
27	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:52844600-52851200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:52844600-52851200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr15:52844600-52856400	Weak transcription	Ovary	ovary
31	chr15:52844600-52859000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr15:52844800-52850400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:52844800-52851000	Weak transcription	Lung	lung
34	chr15:52844800-52851200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:52844800-52851800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:52845200-52851800	Weak transcription	Fetal Intestine Small	intestine
38	chr15:52845200-52854200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:52845200-52857200	Weak transcription	Fetal Stomach	stomach
40	chr15:52845800-52851800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:52845800-52853200	Strong transcription	Primary B cells from cord blood	blood
42	chr15:52846000-52850400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:52846000-52851400	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:52846000-52851600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52846200-52852200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:52846200-52852800	Weak transcription	Stomach Mucosa	stomach
47	chr15:52846200-52855800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr15:52846200-52857200	Weak transcription	Thymus	Thymus
49	chr15:52846200-52859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle

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