Variant report

Variant	rs2462847
Chromosome Location	chr15:52711929-52711930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52711503..52713418-chr15:52716021..52717758,2	K562	blood:
2	chr15:52710263..52712786-chr15:52797709..52799309,2	MCF-7	breast:
3	chr15:52700906..52703355-chr15:52710486..52712910,2	MCF-7	breast:
4	chr15:52692552..52694512-chr15:52711231..52713992,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12438578	0.80[JPT][hapmap]
rs1405183	0.82[AFR][1000 genomes]
rs1405184	0.84[ASW][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs1526169	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1615235	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1669864	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1669866	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1669877	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724585	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1724592	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724593	0.92[YRI][hapmap]
rs1724624	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1724625	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1724626	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724627	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724630	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1724635	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17707852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1972160	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2290332	0.91[MEX][hapmap]
rs2290336	0.91[MEX][hapmap]
rs2444015	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444019	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462848	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2462849	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2600902	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3794557	0.80[AMR][1000 genomes]
rs3794564	0.82[JPT][hapmap];0.85[MEX][hapmap]
rs3794565	0.91[MEX][hapmap]
rs3794566	0.91[MEX][hapmap]
rs7175314	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs7176830	0.80[JPT][hapmap]
rs8030535	0.84[ASW][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes]
rs8033579	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs871488	0.84[ASW][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes]
rs940970	0.84[ASW][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][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	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
3	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
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2462847	MYO5A	cis	cerebellum	SCAN
rs2462847	MYO5A	cis	lymphoblastoid	seeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52665200-52720600	Weak transcription	Pancreas	Pancrea
3	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
4	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:52676400-52721400	Weak transcription	Gastric	stomach
6	chr15:52676600-52718600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
10	chr15:52680600-52719800	Weak transcription	NH-A	brain
11	chr15:52680800-52716400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
14	chr15:52684000-52719800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr15:52684800-52719800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:52685000-52717000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:52687000-52714800	Weak transcription	Psoas Muscle	Psoas
20	chr15:52687000-52715000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
23	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr15:52696000-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:52696200-52719800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:52697200-52715000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:52697200-52718400	Weak transcription	Dnd41	blood
28	chr15:52697200-52720000	Weak transcription	Ovary	ovary
29	chr15:52697200-52730000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:52697200-52730400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
32	chr15:52697400-52720000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:52697400-52730400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:52697600-52720600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:52697800-52715800	Weak transcription	Adipose Nuclei	Adipose
36	chr15:52698600-52720400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:52701400-52713000	Weak transcription	GM12878-XiMat	blood
38	chr15:52702000-52718000	Weak transcription	HSMM	muscle
39	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:52702600-52719800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:52702600-52730000	Weak transcription	Brain Anterior Caudate	brain
42	chr15:52702600-52730600	Weak transcription	Colon Smooth Muscle	Colon
43	chr15:52707200-52719800	Weak transcription	HSMMtube	muscle
44	chr15:52708000-52713600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:52708200-52715800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:52708200-52717800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:52708600-52713400	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:52708600-52714200	Weak transcription	Primary T cells from cord blood	blood
49	chr15:52708600-52715000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:52708800-52720400	Weak transcription	Primary T cells fromperipheralblood	blood

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