Variant report

Variant	rs2049517
Chromosome Location	chr15:52848483-52848484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52820950..52823000-chr15:52846878..52849661,2	MCF-7	breast:
2	chr15:52819620..52821147-chr15:52847308..52848900,2	MCF-7	breast:
3	chr15:52820718..52823193-chr15:52846604..52848495,2	K562	blood:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

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[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1055747	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11539782	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11852533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11853096	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11853137	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11854942	0.88[AMR][1000 genomes]
rs11854997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11855859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11857682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11858238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858875	0.88[CEU][hapmap]
rs17542396	0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17542520	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17542527	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614428	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17614498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17614529	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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3478	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4774633	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776055	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	1.00[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55800146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56947153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.95[AMR][1000 genomes]
rs58185101	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58246435	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60426742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73396714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73396718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73396723	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396728	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396733	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74014300	0.93[AMR][1000 genomes]
rs74016845	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[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
rs2049517	ARPP19	cis	Heart Left Ventricle	GTEx
rs2049517	ARPP19	cis	Muscle Skeletal	GTEx
rs2049517	ARPP19	cis	Adipose Subcutaneous	GTEx
rs2049517	ARPP19	cis	lung	GTEx
rs2049517	ARPP19	cis	Nerve Tibial	GTEx
rs2049517	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs2049517	ARPP19	cis	Artery Tibial	GTEx
rs2049517	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs2049517	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs2049517	ARPP19	cis	Whole Blood	GTEx
rs2049517	ARPP19	cis	Esophagus Muscularis	GTEx
rs2049517	ARPP19	cis	Thyroid	GTEx

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	chr15:52836600-52849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:52837400-52849400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:52837600-52849400	Strong transcription	NHDF-Ad	bronchial
7	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:52838000-52849200	Strong transcription	Osteobl	bone
10	chr15:52838000-52849400	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr15:52838000-52853000	Strong transcription	Dnd41	blood
12	chr15:52838200-52849000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr15:52838200-52849200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:52838200-52849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:52838200-52850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:52838600-52849600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:52838800-52849600	Strong transcription	Hela-S3	cervix
18	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:52839000-52849200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:52839000-52849800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:52839000-52851400	Weak transcription	Gastric	stomach
23	chr15:52839000-52851400	Weak transcription	Spleen	Spleen
24	chr15:52839000-52853400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
27	chr15:52839200-52851000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:52839200-52851000	Weak transcription	Esophagus	oesophagus
29	chr15:52839200-52851800	Weak transcription	Right Ventricle	heart
30	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
31	chr15:52841000-52849200	Strong transcription	HUVEC	blood vessel
32	chr15:52841000-52857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:52841200-52849400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:52841200-52849600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:52841200-52850400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr15:52841400-52849400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
38	chr15:52842800-52851400	Weak transcription	Fetal Heart	heart
39	chr15:52843600-52852600	Weak transcription	Brain Substantia Nigra	brain
40	chr15:52843800-52848800	Weak transcription	Colon Smooth Muscle	Colon
41	chr15:52844000-52849000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:52844200-52849200	Strong transcription	Liver	Liver
43	chr15:52844200-52850400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:52844200-52851000	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:52844200-52852800	Weak transcription	Fetal Brain Female	brain
46	chr15:52844400-52855200	Weak transcription	Fetal Lung	lung
47	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr15:52844600-52851200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:52844600-52851200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:52844600-52856400	Weak transcription	Ovary	ovary

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