Variant report

Variant	rs11858238
Chromosome Location	chr15:52852649-52852650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52852534-52853185	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52585466..52588318-chr15:52852400..52853914,2	MCF-7	breast:
2	chr15:52844956..52846516-chr15:52850734..52853652,2	MCF-7	breast:
3	chr15:52819747..52821438-chr15:52850528..52853277,2	MCF-7	breast:

Variant related genes	Relation type
ARPP19	TF binding region
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1055746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1055747	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11539782	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11852533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11853096	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11853137	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11854942	0.88[AMR][1000 genomes]
rs11854997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855752	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11855859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11857085	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11857682	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857857	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11858875	0.86[CEU][hapmap]
rs17542396	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17542520	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17542527	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17614428	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17614498	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614529	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]
rs2049517	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]
rs2049518	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2899490	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]
rs3478	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4774633	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4776055	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4776056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776057	1.00[CEU][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55800146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56947153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57097265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57167959	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58185101	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58246435	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281006	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60426742	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73396718	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73396723	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396728	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73396733	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73414933	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs74014300	0.93[AMR][1000 genomes]
rs74016845	0.92[AFR][1000 genomes];0.91[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11858238	ARPP19	cis	Thyroid	GTEx
rs11858238	ARPP19	cis	Artery Tibial	GTEx
rs11858238	ARPP19	cis	Whole Blood	GTEx
rs11858238	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs11858238	ARPP19	cis	Nerve Tibial	GTEx
rs11858238	ARPP19	cis	Esophagus Muscularis	GTEx
rs11858238	ARPP19	cis	Muscle Skeletal	GTEx
rs11858238	ARPP19	cis	Adipose Subcutaneous	GTEx
rs11858238	ARPP19	cis	lung	GTEx
rs11858238	ARPP19	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
2	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:52838000-52853000	Strong transcription	Dnd41	blood
4	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:52839000-52853400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:52839000-52858400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:52839000-52859600	Weak transcription	Aorta	Aorta
9	chr15:52839200-52859200	Weak transcription	Colonic Mucosa	Colon
10	chr15:52841000-52857400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:52842400-52858400	Weak transcription	Pancreas	Pancrea
12	chr15:52844200-52852800	Weak transcription	Fetal Brain Female	brain
13	chr15:52844400-52855200	Weak transcription	Fetal Lung	lung
14	chr15:52844400-52859200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:52844600-52856400	Weak transcription	Ovary	ovary
16	chr15:52844600-52859000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:52844800-52860000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:52845200-52854200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:52845200-52857200	Weak transcription	Fetal Stomach	stomach
20	chr15:52845800-52853200	Strong transcription	Primary B cells from cord blood	blood
21	chr15:52846200-52852800	Weak transcription	Stomach Mucosa	stomach
22	chr15:52846200-52855800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:52846200-52857200	Weak transcription	Thymus	Thymus
24	chr15:52846200-52859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:52846200-52860000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:52847000-52859400	Weak transcription	Fetal Intestine Large	intestine
27	chr15:52847800-52853000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52848200-52853200	Genic enhancers	K562	blood
29	chr15:52849000-52852800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:52849400-52852800	Weak transcription	Brain Angular Gyrus	brain
31	chr15:52849400-52852800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:52849400-52853000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr15:52849400-52857200	Weak transcription	Fetal Thymus	thymus
34	chr15:52849400-52857400	Weak transcription	Primary T cells from cord blood	blood
35	chr15:52849400-52857400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr15:52849400-52859000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:52849400-52860000	Weak transcription	Placenta	Placenta
38	chr15:52849600-52853400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:52849600-52853400	Enhancers	Colon Smooth Muscle	Colon
40	chr15:52849600-52857400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:52849800-52855800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:52849800-52857200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:52850000-52852800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:52850000-52853400	Enhancers	NH-A	brain
45	chr15:52850000-52859200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:52850200-52853200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:52850200-52853400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr15:52850200-52853600	Genic enhancers	A549	lung
49	chr15:52850200-52858200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:52850200-52859200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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