Variant report

Variant	rs1724591
Chromosome Location	chr15:52739293-52739294
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1001522	0.94[AFR][1000 genomes]
rs10083671	0.93[ASN][1000 genomes]
rs12898655	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1464964	0.92[AFR][1000 genomes]
rs1669856	0.90[AFR][1000 genomes]
rs1669858	0.92[AFR][1000 genomes]
rs1669867	0.84[AFR][1000 genomes]
rs1724589	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1724628	0.91[AFR][1000 genomes]
rs1724629	0.91[AFR][1000 genomes]
rs1724631	0.92[AFR][1000 genomes]
rs1724634	0.88[AFR][1000 genomes]
rs1724639	0.85[AFR][1000 genomes]
rs1724641	0.96[AFR][1000 genomes]
rs2414151	0.92[AFR][1000 genomes]
rs2444013	0.92[AFR][1000 genomes]
rs2950056	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35523401	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3858907	0.92[AFR][1000 genomes]
rs71474804	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7176061	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs722436	0.92[AFR][1000 genomes]
rs935892	0.89[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1724591	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs1724591	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

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	chr15:52729000-52739400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:52730400-52744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:52730600-52739400	Weak transcription	Esophagus	oesophagus
6	chr15:52730600-52741600	Weak transcription	Ovary	ovary
7	chr15:52730600-52741600	Weak transcription	HUVEC	blood vessel
8	chr15:52730600-52741800	Weak transcription	Gastric	stomach
9	chr15:52730800-52741800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:52734400-52740400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:52734400-52743800	Weak transcription	Brain Angular Gyrus	brain
13	chr15:52734600-52741600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:52734600-52753200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:52734800-52739800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:52734800-52740000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:52734800-52740200	Weak transcription	HSMMtube	muscle
18	chr15:52734800-52743800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:52734800-52747400	Weak transcription	HSMM	muscle
20	chr15:52735400-52740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr15:52736000-52739400	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr15:52736600-52740800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:52737200-52740400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr15:52737200-52740600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr15:52737200-52742000	Enhancers	Adipose Nuclei	Adipose
26	chr15:52737800-52740000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr15:52738000-52739400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:52738000-52743800	Weak transcription	Brain Anterior Caudate	brain
29	chr15:52738200-52740000	Weak transcription	Brain Substantia Nigra	brain
30	chr15:52738200-52741600	Weak transcription	Pancreas	Pancrea
31	chr15:52738400-52739400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:52738400-52740000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr15:52738400-52740000	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:52738600-52739800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr15:52738600-52740200	Weak transcription	Right Ventricle	heart
36	chr15:52738600-52741600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr15:52738800-52740000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:52738800-52740000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:52738800-52740200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:52738800-52740600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:52738800-52741800	Weak transcription	Psoas Muscle	Psoas
42	chr15:52738800-52744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr15:52739000-52740200	Weak transcription	Left Ventricle	heart
44	chr15:52739000-52741800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:52739000-52751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:52739000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:52739200-52739600	Weak transcription	Right Atrium	heart
48	chr15:52739200-52740200	Weak transcription	Brain Hippocampus Middle	brain

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