Variant report

Variant	rs2444019
Chromosome Location	chr15:52731198-52731199
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	YY1	chr15:52731126-52731657	H1-hESC	embryonic stem cell:	n/a	chr15:52731399-52731411 chr15:52731421-52731433

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52730099..52731803-chr15:52755722..52757493,2	MCF-7	breast:

Variant related genes	Relation type
MYO5A	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1526169	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534200	0.83[AFR][1000 genomes]
rs1615235	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1669864	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669866	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1669877	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724585	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1724592	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1724624	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1724625	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1724626	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724627	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724630	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1724635	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17707852	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1972160	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2444015	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462847	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462848	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2462849	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2600902	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8033579	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2444019	MYO5A	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
2	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
3	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
4	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:52710800-52732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:52711600-52732000	Weak transcription	Brain Germinal Matrix	brain
7	chr15:52716600-52732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:52720200-52732200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:52720800-52732400	Weak transcription	NHDF-Ad	bronchial
10	chr15:52721000-52732200	Weak transcription	HSMMtube	muscle
11	chr15:52721000-52732800	Weak transcription	NH-A	brain
12	chr15:52721000-52733200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:52721400-52732000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:52721400-52732200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:52721400-52737800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:52721400-52739000	Weak transcription	Primary B cells from cord blood	blood
17	chr15:52724600-52733600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:52728600-52737400	Weak transcription	Psoas Muscle	Psoas
19	chr15:52729000-52739400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr15:52729200-52734800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:52729800-52734800	Enhancers	Adipose Nuclei	Adipose
22	chr15:52730000-52731200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:52730000-52731400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr15:52730000-52731400	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr15:52730000-52731800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:52730000-52734200	Enhancers	Brain Cingulate Gyrus	brain
27	chr15:52730000-52735600	Enhancers	Brain Anterior Caudate	brain
28	chr15:52730200-52731200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr15:52730200-52731200	Enhancers	H9 Cell Line	embryonic stem cell
30	chr15:52730200-52732600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:52730200-52734800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:52730400-52731200	Enhancers	H1 Cell Line	embryonic stem cell
33	chr15:52730400-52731200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:52730400-52731200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr15:52730400-52731200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:52730400-52731200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr15:52730400-52731200	Enhancers	Right Atrium	heart
38	chr15:52730400-52731800	Weak transcription	HMEC	breast
39	chr15:52730400-52732600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:52730400-52744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:52730600-52731600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr15:52730600-52731600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:52730600-52731800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:52730600-52731800	Weak transcription	Brain Substantia Nigra	brain
45	chr15:52730600-52731800	Weak transcription	Left Ventricle	heart
46	chr15:52730600-52732200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:52730600-52732200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr15:52730600-52732200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:52730600-52732800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:52730600-52733000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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