Variant report

Variant	rs1526169
Chromosome Location	chr15:52720908-52720909
allele	G/T
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	KAP1	chr15:52719824-52721014	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52718660..52721440-chr15:52817990..52820866,2	MCF-7	breast:

Variant related genes	Relation type
MYO5A	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1405184	0.82[MEX][hapmap]
rs1534200	0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1615235	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1669864	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669866	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1669877	0.94[ASW][hapmap];0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1693494	0.82[YRI][hapmap]
rs1724585	0.90[EUR][1000 genomes]
rs1724592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1724593	0.82[TSI][hapmap]
rs1724595	0.82[YRI][hapmap]
rs1724624	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1724625	0.83[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1724626	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724627	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724630	0.90[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1724635	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17707852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972160	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2257152	0.82[YRI][hapmap]
rs2290332	0.82[MEX][hapmap]
rs2290336	0.82[MEX][hapmap]
rs2444015	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2444019	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2462847	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]
rs2462848	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2462849	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2600902	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2693462	0.90[LWK][hapmap]
rs3794564	0.82[MEX][hapmap]
rs3794565	0.82[MEX][hapmap]
rs3794566	0.82[MEX][hapmap]
rs7175314	0.80[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs8030535	0.86[MEX][hapmap]
rs8033579	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs871488	0.82[MEX][hapmap]
rs940970	0.82[MEX][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1526169	MYO5A	cis	lymphoblastoid	seeQTL
rs1526169	MYO5A	cis	Artery Tibial	GTEx
rs1526169	MYO5A	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
2	chr15:52668800-52730400	Weak transcription	Aorta	Aorta
3	chr15:52673800-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:52676400-52721400	Weak transcription	Gastric	stomach
5	chr15:52677000-52730000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:52679800-52729600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:52679800-52740000	Weak transcription	Spleen	Spleen
8	chr15:52680800-52730000	Weak transcription	Brain Angular Gyrus	brain
9	chr15:52680800-52740200	Weak transcription	Thymus	Thymus
10	chr15:52684800-52730000	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:52685400-52730000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr15:52689600-52730200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr15:52689600-52730200	Weak transcription	Left Ventricle	heart
14	chr15:52689600-52730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:52696000-52730200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:52697200-52730000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:52697200-52730400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:52697200-52738600	Weak transcription	Fetal Brain Female	brain
19	chr15:52697400-52730400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:52702400-52737600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:52702600-52730000	Weak transcription	Brain Anterior Caudate	brain
22	chr15:52702600-52730600	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:52710800-52732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:52711600-52732000	Weak transcription	Brain Germinal Matrix	brain
25	chr15:52713600-52721000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:52713600-52729800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:52714800-52722600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:52715600-52726400	Weak transcription	Psoas Muscle	Psoas
29	chr15:52716600-52722600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:52716600-52732600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:52716800-52721400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:52717000-52721400	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:52717200-52721400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr15:52717200-52730200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:52717800-52722800	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:52719000-52728000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:52719400-52722600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr15:52719600-52721200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:52719600-52722600	Weak transcription	Brain Substantia Nigra	brain
40	chr15:52719800-52721000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:52719800-52721000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:52719800-52721000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:52719800-52721000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr15:52719800-52721000	Enhancers	HSMMtube	muscle
45	chr15:52719800-52721000	Enhancers	NH-A	brain
46	chr15:52719800-52721000	Enhancers	Osteobl	bone
47	chr15:52719800-52722600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:52719800-52722800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:52720000-52721000	Strong transcription	Primary T cells from cord blood	blood
50	chr15:52720000-52721000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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