Variant report

Variant	rs2290334
Chromosome Location	chr15:52615712-52615713
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1045700	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs10518684	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10518689	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10518691	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10518692	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1058219	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11852261	0.84[EUR][1000 genomes]
rs11853078	0.82[JPT][hapmap]
rs11853114	0.90[CEU][hapmap];0.92[CHB][hapmap]
rs11853337	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11853586	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11853802	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11854130	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11854247	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11854673	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs11854780	0.91[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap]
rs11854886	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11855082	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11855453	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11855584	0.88[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11855820	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11855884	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11856588	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11856662	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11856752	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs11856810	0.94[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11856896	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11857993	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11858031	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12050602	0.83[ASN][1000 genomes]
rs12050717	0.87[ASN][1000 genomes]
rs1464965	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1464966	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1474435	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1474436	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1474437	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1474438	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1693492	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs1693494	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs1693497	0.93[CEU][hapmap];0.92[CHB][hapmap]
rs1693501	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1693502	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1693506	0.93[CEU][hapmap];0.87[CHB][hapmap]
rs1724578	0.91[EUR][1000 genomes]
rs1724579	0.91[EUR][1000 genomes]
rs1724595	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs1724603	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs1724608	0.84[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs1724638	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs17541809	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17613587	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17613607	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17613951	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17651212	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17651218	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17651230	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17651242	0.84[EUR][1000 genomes]
rs17651326	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs17651611	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs17651631	0.93[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs17707338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17707651	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17707705	0.84[EUR][1000 genomes]
rs17707729	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17707996	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs17708103	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1815176	0.82[EUR][1000 genomes]
rs1869126	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1869127	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1869128	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2140962	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2177876	0.93[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2257152	0.94[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs2272283	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs2414148	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2693462	0.94[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap]
rs2899488	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs35943650	0.93[EUR][1000 genomes]
rs3751619	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3751620	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs3794568	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816449	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41408650	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs4341694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774623	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4774624	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap]
rs4774625	0.92[CEU][hapmap];0.92[CHB][hapmap];0.83[JPT][hapmap]
rs4774627	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4776044	0.93[EUR][1000 genomes]
rs4776045	0.93[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs4776051	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs55722736	0.82[EUR][1000 genomes]
rs55978431	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56128753	0.84[EUR][1000 genomes]
rs56136255	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56312354	0.90[ASN][1000 genomes]
rs56992654	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58043289	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59496859	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59584964	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs68155341	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72623980	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72736668	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72736669	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs940966	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[EUR][1000 genomes]
rs940967	0.92[EUR][1000 genomes]
rs940971	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs940972	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs940973	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9788691	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2290334	ARPP19	cis	Nerve Tibial	GTEx
rs2290334	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs2290334	MYO5A	cis	multi-tissue	Pritchard
rs2290334	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:52600600-52624200	Weak transcription	Liver	Liver
6	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:52601800-52616600	Strong transcription	Primary B cells from cord blood	blood
14	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
15	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
18	chr15:52603200-52616400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:52605400-52622800	Strong transcription	HSMMtube	muscle
20	chr15:52606800-52618600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
23	chr15:52608200-52615800	Strong transcription	Adipose Nuclei	Adipose
24	chr15:52608600-52615800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr15:52608600-52616800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:52608600-52622400	Strong transcription	GM12878-XiMat	blood
27	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:52609000-52619600	Weak transcription	HepG2	liver
29	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
30	chr15:52609600-52618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:52609800-52622000	Weak transcription	Osteobl	bone
32	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
34	chr15:52610200-52615800	Strong transcription	Brain Anterior Caudate	brain
35	chr15:52611400-52620600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:52611600-52615800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:52611600-52615800	Weak transcription	HMEC	breast
40	chr15:52611600-52617200	Weak transcription	Left Ventricle	heart
41	chr15:52611600-52617600	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr15:52611600-52618600	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:52611600-52618600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:52611600-52618600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:52611600-52620200	Weak transcription	Fetal Brain Male	brain
46	chr15:52611600-52620800	Weak transcription	Pancreas	Pancrea
47	chr15:52611600-52621000	Weak transcription	Right Atrium	heart
48	chr15:52611600-52621200	Weak transcription	NHDF-Ad	bronchial
49	chr15:52611600-52621600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:52611600-52621800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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