Variant report

Variant	rs3751620
Chromosome Location	chr15:52601570-52601571
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52599470..52602451-chr15:52610830..52612789,2	K562	blood:
2	chr15:52532801..52535731-chr15:52601515..52603297,2	MCF-7	breast:
3	chr15:52590879..52593445-chr15:52599970..52603838,3	MCF-7	breast:
4	chr15:52600034..52602516-chr15:52612985..52614649,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAPK6-8	chr15:52600575-52601909	NONHSAT043927

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10518684	0.86[CHB][hapmap]
rs10518689	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10518691	0.88[CEU][hapmap]
rs1058219	0.94[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs11853078	0.92[JPT][hapmap]
rs11853114	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs11853337	0.88[CEU][hapmap]
rs11853586	0.94[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11854130	0.88[CEU][hapmap]
rs11854247	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11854886	0.83[EUR][1000 genomes]
rs11855082	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs11855453	0.88[CEU][hapmap]
rs11855584	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs11855820	0.88[CEU][hapmap]
rs11855884	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs11856588	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11856662	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11856752	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs11856810	0.88[CEU][hapmap]
rs11856896	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs11857993	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11858031	0.88[CEU][hapmap]
rs1464965	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1464966	0.88[CEU][hapmap]
rs1474437	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1474438	0.88[CEU][hapmap]
rs1693492	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1693494	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1693497	0.86[CEU][hapmap];0.84[CHB][hapmap]
rs1724578	0.84[EUR][1000 genomes]
rs1724579	0.84[EUR][1000 genomes]
rs1724638	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs17541809	0.85[EUR][1000 genomes]
rs17613587	0.89[EUR][1000 genomes]
rs17613607	0.89[EUR][1000 genomes]
rs17613951	0.83[EUR][1000 genomes]
rs17651611	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17651631	0.86[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs17707338	0.89[EUR][1000 genomes]
rs17707996	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs1869126	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs1869127	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs1869128	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2140962	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2177876	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2257152	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2272283	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs2290334	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs2414148	0.94[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes]
rs2693462	0.88[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2899488	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs35943650	0.84[EUR][1000 genomes]
rs3751619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3794568	0.85[EUR][1000 genomes]
rs3816449	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs41408650	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4341694	0.94[CEU][hapmap];0.93[CHB][hapmap];0.90[EUR][1000 genomes]
rs4774623	0.83[EUR][1000 genomes]
rs4774624	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4774625	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap]
rs4774627	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs4776044	0.82[EUR][1000 genomes]
rs4776045	0.87[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs4776051	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs55978431	0.85[EUR][1000 genomes]
rs56136255	0.83[EUR][1000 genomes]
rs56992654	0.83[EUR][1000 genomes]
rs59496859	0.83[EUR][1000 genomes]
rs59584964	0.83[EUR][1000 genomes]
rs68155341	0.85[EUR][1000 genomes]
rs940966	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs940967	0.85[EUR][1000 genomes]
rs940971	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs940972	0.87[CEU][hapmap];0.86[CHB][hapmap]
rs940973	0.87[CEU][hapmap];0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3751620	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs3751620	MYO5A	cis	multi-tissue	Pritchard
rs3751620	MYO5A	cis	Lymphoblastoid	GTEx
rs3751620	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52588200-52602200	Weak transcription	HSMM	muscle
2	chr15:52588400-52602800	Weak transcription	Aorta	Aorta
3	chr15:52591200-52602400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:52593600-52608600	Weak transcription	Fetal Brain Male	brain
5	chr15:52595200-52601600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:52595200-52605600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:52595400-52605600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:52595400-52610800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:52595400-52614200	Weak transcription	Fetal Lung	lung
10	chr15:52595600-52603400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:52595600-52609800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52595800-52601600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:52595800-52602000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:52596000-52601600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:52596000-52601600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr15:52596000-52602200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr15:52596000-52603000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:52596000-52604800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:52596000-52605000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:52596000-52605000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:52596000-52608400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:52596000-52608800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:52596000-52611000	Weak transcription	Fetal Stomach	stomach
25	chr15:52596200-52602800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr15:52596400-52605000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:52596400-52608600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr15:52597600-52608600	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr15:52598200-52602800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:52598400-52608400	Weak transcription	Brain Hippocampus Middle	brain
34	chr15:52598800-52601600	Weak transcription	HSMMtube	muscle
35	chr15:52598800-52602800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:52598800-52604400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr15:52599000-52601800	Weak transcription	Osteobl	bone
38	chr15:52599000-52605200	Weak transcription	HMEC	breast
39	chr15:52599000-52605200	Weak transcription	NHEK	skin
40	chr15:52599200-52602800	Weak transcription	Brain Substantia Nigra	brain
41	chr15:52599200-52605000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:52599200-52611000	Weak transcription	NHLF	lung
43	chr15:52599400-52601800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:52599400-52601800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:52599400-52611000	Weak transcription	Fetal Thymus	thymus
46	chr15:52599400-52611000	Weak transcription	Thymus	Thymus
47	chr15:52599600-52601600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr15:52599600-52605400	Weak transcription	Brain Germinal Matrix	brain
49	chr15:52599800-52601600	Weak transcription	Esophagus	oesophagus
50	chr15:52599800-52611000	Weak transcription	Rectal Mucosa Donor 31	rectum

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