Variant report

Variant	rs3478
Chromosome Location	chr15:52843442-52843443
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52842839..52845667-chr15:52845683..52848317,2	K562	blood:
2	chr15:52836622..52839186-chr15:52841792..52845841,4	K562	blood:
3	chr15:52837261..52840412-chr15:52840986..52844425,3	K562	blood:
4	chr15:52842678..52845632-chr15:52848301..52850165,2	MCF-7	breast:
5	chr15:52837831..52839348-chr15:52842783..52844541,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 51 )
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];0.96[EUR][1000 genomes]
rs1055747	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11539782	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11852533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11853096	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11853137	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11854942	0.88[AMR][1000 genomes]
rs11854997	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11855752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11855859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11857085	1.00[CEU][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11857682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11857857	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11858238	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11858875	0.88[CEU][hapmap]
rs17542396	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17542520	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17542527	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17614428	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17614529	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2049517	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2049518	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2899490	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];0.99[EUR][1000 genomes]
rs4776055	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4776056	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4776057	1.00[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55800146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56947153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57097265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57167959	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58185101	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58246435	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59281006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60426742	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73396714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73396718	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73396723	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73396728	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73396733	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73414932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73414933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74014300	0.93[AMR][1000 genomes]
rs74016845	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	esv1001541	chr15:52839342-52843856	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3478	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs3478	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs3478	ARPP19	cis	Thyroid	GTEx
rs3478	ARPP19	cis	Skin Sun Exposed Lower leg	GTEx
rs3478	ARPP19	cis	Esophagus Muscularis	GTEx
rs3478	ARPP19	cis	lung	GTEx
rs3478	ARPP19	cis	Muscle Skeletal	GTEx
rs3478	ARPP19	cis	Adipose Subcutaneous	GTEx
rs3478	ARPP19	cis	Whole Blood	GTEx
rs3478	ARPP19	cis	Artery Tibial	GTEx
rs3478	ARPP19	cis	Nerve Tibial	GTEx
rs3478	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	chr15:52828800-52850400	Weak transcription	Fetal Brain Male	brain
2	chr15:52835800-52845800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:52836200-52851400	Weak transcription	Fetal Kidney	kidney
4	chr15:52836400-52855200	Weak transcription	Small Intestine	intestine
5	chr15:52836600-52844000	Weak transcription	K562	blood
6	chr15:52836600-52844200	Weak transcription	Psoas Muscle	Psoas
7	chr15:52836600-52846000	Weak transcription	Stomach Mucosa	stomach
8	chr15:52836600-52849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:52836800-52848200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:52837200-52844800	Strong transcription	A549	lung
11	chr15:52837400-52844000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:52837400-52844600	Strong transcription	HSMM	muscle
13	chr15:52837400-52847000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:52837400-52849400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:52837600-52849400	Strong transcription	NHDF-Ad	bronchial
16	chr15:52837600-52852000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:52837800-52846000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:52837800-52853000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:52838000-52844000	Strong transcription	Adipose Nuclei	Adipose
20	chr15:52838000-52844600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:52838000-52845200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:52838000-52846200	Strong transcription	Primary T cells from cord blood	blood
23	chr15:52838000-52846800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:52838000-52847000	Strong transcription	Fetal Thymus	thymus
25	chr15:52838000-52849200	Strong transcription	Osteobl	bone
26	chr15:52838000-52849400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:52838000-52853000	Strong transcription	Dnd41	blood
28	chr15:52838200-52844600	Strong transcription	NHEK	skin
29	chr15:52838200-52844800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:52838200-52845800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr15:52838200-52849000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:52838200-52849200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:52838200-52849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:52838200-52850000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:52838400-52845000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr15:52838400-52846000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:52838400-52846200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr15:52838600-52844600	Strong transcription	Placenta	Placenta
39	chr15:52838600-52845400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:52838600-52846200	Strong transcription	Thymus	Thymus
41	chr15:52838600-52847000	Strong transcription	Fetal Intestine Large	intestine
42	chr15:52838600-52849600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr15:52838800-52844800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr15:52838800-52849600	Strong transcription	Hela-S3	cervix
45	chr15:52838800-52859800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:52838800-52860000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:52839000-52844000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:52839000-52844000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:52839000-52844000	Weak transcription	Fetal Intestine Small	intestine
50	chr15:52839000-52849200	Weak transcription	Rectal Smooth Muscle	rectum

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