Variant report

Variant	rs2600902
Chromosome Location	chr15:52747615-52747616
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52746584..52749039-chr15:52819841..52822559,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction

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

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

rs_ID	r²[population]
rs1526169	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1534200	0.82[ASN][1000 genomes]
rs1615235	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1669864	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1669866	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1669877	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1724585	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1724592	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1724624	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1724625	0.85[AFR][1000 genomes]
rs1724626	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1724627	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1724630	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1724635	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17707852	0.87[EUR][1000 genomes]
rs1972160	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2444015	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2444019	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2462847	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2462848	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2462849	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8033579	0.81[EUR][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
rs2600902	MYO5A	cis	Artery Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:52734600-52753200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:52739000-52751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:52739000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:52740400-52756200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:52740600-52753200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr15:52742000-52755800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:52742200-52751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:52742200-52753000	Weak transcription	NHEK	skin
10	chr15:52743800-52758200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:52744600-52749200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:52747400-52747800	ZNF genes & repeats	HSMM	muscle
13	chr15:52747400-52753200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:52747600-52747800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:52747600-52748400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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