Variant report

Variant	rs1059513
Chromosome Location	chr12:57489709-57489710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10506348	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs11172086	0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs3024971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3741578	0.92[JPT][hapmap]
rs725956	0.84[JPT][hapmap]
rs7958413	0.92[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

Variant related diseases (count:3)

Disease	PMID	Source
Allergic sensitization	23817571	GWAS catalog
IgE levels	22075330	GWAS catalog
Sensory disturbances after bilateral sagittal split ramus osteotomy	23834954	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1059513	CDK4,TSPAN31	cis	intralobular white matter	BrainEAC
rs1059513	TSPAN31	cis	intralobular white matter	BrainEAC
rs1059513	STAT6	cis	lymphoblastoid	seeQTL
rs1059513	OS9	cis	intralobular white matter	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57483800-57492000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:57484000-57498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:57484400-57490800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:57484400-57491000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:57484800-57490800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:57485000-57490800	Genic enhancers	Fetal Thymus	thymus
7	chr12:57485000-57491000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:57485000-57491000	Genic enhancers	Fetal Muscle Trunk	muscle
9	chr12:57485000-57491400	Strong transcription	Aorta	Aorta
10	chr12:57485200-57489800	Strong transcription	HepG2	liver
11	chr12:57485200-57490000	Genic enhancers	NH-A	brain
12	chr12:57485400-57491000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:57485400-57491200	Strong transcription	Fetal Intestine Large	intestine
14	chr12:57485600-57490600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:57485800-57490000	Strong transcription	Gastric	stomach
16	chr12:57486000-57489800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:57486200-57503600	Weak transcription	Fetal Brain Male	brain
18	chr12:57486600-57503800	Weak transcription	Brain Substantia Nigra	brain
19	chr12:57486800-57491200	Weak transcription	Hela-S3	cervix
20	chr12:57487200-57490400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:57487200-57491000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:57487200-57491000	Genic enhancers	Esophagus	oesophagus
23	chr12:57487200-57491000	Genic enhancers	NHEK	skin
24	chr12:57487600-57490800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:57487600-57491000	Genic enhancers	HMEC	breast
26	chr12:57487600-57501400	Weak transcription	Right Atrium	heart
27	chr12:57487600-57503600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:57487800-57490000	Strong transcription	Brain Germinal Matrix	brain
29	chr12:57487800-57490400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr12:57487800-57490400	Genic enhancers	HUES6 Cell Line	embryonic stem cell
31	chr12:57487800-57490400	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr12:57487800-57490600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:57487800-57490800	Genic enhancers	GM12878-XiMat	blood
34	chr12:57487800-57491000	Weak transcription	Psoas Muscle	Psoas
35	chr12:57487800-57493000	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:57487800-57494400	Strong transcription	Dnd41	blood
37	chr12:57487800-57495000	Strong transcription	Thymus	Thymus
38	chr12:57488200-57490200	Weak transcription	Small Intestine	intestine
39	chr12:57488200-57490400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:57488200-57491000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:57488200-57492400	Weak transcription	Fetal Heart	heart
42	chr12:57488200-57494800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr12:57488400-57489800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:57488400-57490000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr12:57488400-57490400	Strong transcription	Fetal Brain Female	brain
46	chr12:57488400-57490800	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr12:57488400-57492600	Weak transcription	Stomach Mucosa	stomach
48	chr12:57488400-57492600	Strong transcription	Spleen	Spleen
49	chr12:57488400-57493000	Genic enhancers	K562	blood
50	chr12:57488400-57494000	Strong transcription	Left Ventricle	heart

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