Variant report

Variant	rs752864
Chromosome Location	chr15:52631991-52631992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52629612..52632339-chr15:52635777..52638490,2	K562	blood:
2	chr15:52630806..52632782-chr15:52635293..52638490,3	K562	blood:
3	chr15:52586748..52589212-chr15:52631560..52633656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1001522	0.83[CHB][hapmap]
rs10083673	0.90[CHB][hapmap]
rs1009157	0.82[AMR][1000 genomes]
rs10467925	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12324100	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12324121	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs12914979	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1464963	0.90[CHB][hapmap]
rs1669858	0.91[CHB][hapmap]
rs1669867	0.90[CHB][hapmap]
rs1724628	0.81[CHB][hapmap]
rs1724629	0.90[CHB][hapmap]
rs1724641	0.83[CHB][hapmap]
rs2242057	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2242058	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2414150	0.90[CHB][hapmap]
rs2414151	0.81[CHB][hapmap]
rs4280181	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs4519295	0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs4606660	0.82[ASN][1000 genomes]
rs4776037	0.82[AMR][1000 genomes]
rs4776039	0.80[AMR][1000 genomes]
rs62015999	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176061	0.83[CHB][hapmap]
rs7176482	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs7176639	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182150	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs752865	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752866	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028033	0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8033626	0.80[AMR][1000 genomes]
rs8038386	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs935892	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs752864	MYO5A	cis	intralobular white matter	BrainEAC
rs752864	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs752864	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
5	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
7	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:52611800-52675800	Weak transcription	Gastric	stomach
9	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
11	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
12	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
13	chr15:52619200-52632000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:52619600-52632000	Weak transcription	Brain Germinal Matrix	brain
15	chr15:52619800-52640600	Weak transcription	Left Ventricle	heart
16	chr15:52619800-52641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:52620000-52632000	Weak transcription	Lung	lung
18	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung
20	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
21	chr15:52621800-52640200	Weak transcription	Fetal Brain Female	brain
22	chr15:52621800-52662200	Weak transcription	Psoas Muscle	Psoas
23	chr15:52622400-52632000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:52622400-52632000	Weak transcription	Pancreas	Pancrea
25	chr15:52622400-52636000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:52622600-52632000	Weak transcription	Aorta	Aorta
27	chr15:52622600-52632000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr15:52623800-52644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:52624200-52632000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:52624200-52632000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:52624200-52632000	Weak transcription	Thymus	Thymus
32	chr15:52624200-52632200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:52624200-52632200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:52624200-52636200	Weak transcription	Fetal Heart	heart
35	chr15:52624200-52641200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:52624400-52632000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:52624400-52636600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:52624400-52636600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr15:52624600-52632000	Weak transcription	Dnd41	blood
40	chr15:52624600-52641200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:52624600-52641400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:52624600-52642400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:52626600-52632600	Strong transcription	Adipose Nuclei	Adipose
44	chr15:52627000-52646600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:52627200-52641200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:52627400-52632000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr15:52627400-52641400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:52627600-52632000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:52628400-52632000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:52628600-52632600	Enhancers	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links