Variant report

Variant	rs35523401
Chromosome Location	chr15:52741854-52741855
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1001522	0.93[ASN][1000 genomes]
rs10083673	0.94[ASN][1000 genomes]
rs10518687	0.87[ASN][1000 genomes]
rs1125460	0.89[ASN][1000 genomes]
rs12898655	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12909874	0.98[ASN][1000 genomes]
rs1464963	0.94[ASN][1000 genomes]
rs1464964	0.94[ASN][1000 genomes]
rs1669856	0.94[ASN][1000 genomes]
rs1669858	0.94[ASN][1000 genomes]
rs1669867	0.88[ASN][1000 genomes]
rs1724589	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1724591	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1724628	0.89[ASN][1000 genomes]
rs1724629	0.89[ASN][1000 genomes]
rs1724631	0.94[ASN][1000 genomes]
rs1724634	0.94[ASN][1000 genomes]
rs1724639	0.98[ASN][1000 genomes]
rs1724641	0.98[ASN][1000 genomes]
rs17542017	0.89[ASN][1000 genomes]
rs2414150	0.92[ASN][1000 genomes]
rs2414151	0.89[ASN][1000 genomes]
rs2444013	0.89[ASN][1000 genomes]
rs2950056	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35134548	0.88[ASN][1000 genomes]
rs3858907	0.89[ASN][1000 genomes]
rs4776046	0.98[ASN][1000 genomes]
rs62023267	0.94[ASN][1000 genomes]
rs71474804	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs722436	0.90[ASN][1000 genomes]
rs935892	0.89[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs35523401	MYO5A	Cis_1M	lymphoblastoid	RTeQTL
rs35523401	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52730400-52744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr15:52732600-52750600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:52734400-52743800	Weak transcription	Brain Angular Gyrus	brain
4	chr15:52734600-52753200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:52734800-52743800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:52734800-52747400	Weak transcription	HSMM	muscle
7	chr15:52737200-52742000	Enhancers	Adipose Nuclei	Adipose
8	chr15:52738000-52743800	Weak transcription	Brain Anterior Caudate	brain
9	chr15:52738800-52744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr15:52739000-52751800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:52739000-52753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr15:52739600-52742200	Enhancers	Right Atrium	heart
13	chr15:52740200-52742200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr15:52740200-52742400	Enhancers	Left Ventricle	heart
15	chr15:52740400-52742000	Weak transcription	Spleen	Spleen
16	chr15:52740400-52756200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:52740600-52744200	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:52740600-52753200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr15:52740800-52742400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:52741000-52742000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:52741000-52743400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:52741200-52743800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:52741400-52743000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:52741600-52742000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr15:52741600-52742000	Enhancers	HUVEC	blood vessel
26	chr15:52741600-52742200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:52741600-52742200	Enhancers	Pancreas	Pancrea
28	chr15:52741600-52742200	Enhancers	Right Ventricle	heart
29	chr15:52741600-52742200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:52741600-52742400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr15:52741800-52742000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:52741800-52742000	Enhancers	Primary B cells from peripheral blood	blood
33	chr15:52741800-52742000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr15:52741800-52742000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:52741800-52742000	Enhancers	Brain Substantia Nigra	brain
36	chr15:52741800-52742200	Enhancers	Gastric	stomach
37	chr15:52741800-52742200	Enhancers	Psoas Muscle	Psoas
38	chr15:52741800-52743600	Weak transcription	Brain Cingulate Gyrus	brain

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