Variant report

Variant	rs10492059
Chromosome Location	chr12:4931859-4931860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10849147	0.89[AFR][1000 genomes]
rs10849148	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177303	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs17783823	0.81[CHB][hapmap]
rs17783925	0.85[ASN][1000 genomes]
rs56021447	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57928290	0.85[ASN][1000 genomes]
rs57945693	0.85[ASN][1000 genomes]
rs60191275	0.85[ASN][1000 genomes]
rs7313171	0.80[ASN][1000 genomes]

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	nsv520570	chr12:4929787-4954591	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1047238	chr12:4929787-4955435	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10492059	TSPAN9	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4925200-4932000	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:4925600-4934600	Enhancers	Primary B cells from cord blood	blood
3	chr12:4926400-4939000	Weak transcription	Spleen	Spleen
4	chr12:4927400-4934400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:4927400-4935400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:4927800-4933200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:4927800-4933200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:4927800-4938800	Weak transcription	Brain Germinal Matrix	brain
9	chr12:4928000-4935800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:4928200-4932400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:4928200-4933400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:4928400-4932000	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:4928400-4933200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:4929000-4934800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:4929000-4939200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:4929200-4933200	Weak transcription	Thymus	Thymus
17	chr12:4929200-4934000	Weak transcription	Primary T cells from cord blood	blood
18	chr12:4929200-4966600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:4929400-4933200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:4929400-4934000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:4929400-4937800	Weak transcription	Fetal Brain Female	brain
22	chr12:4929400-4966600	Weak transcription	Brain Angular Gyrus	brain
23	chr12:4929800-4933800	Weak transcription	Fetal Thymus	thymus
24	chr12:4930400-4934200	Weak transcription	GM12878-XiMat	blood
25	chr12:4930400-4935600	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:4930600-4934800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:4930600-4938800	Weak transcription	Fetal Stomach	stomach
28	chr12:4930800-4933000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:4930800-4942400	Weak transcription	Fetal Brain Male	brain
30	chr12:4931000-4932000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:4931000-4937600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:4931400-4933200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:4931600-4932000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr12:4931600-4932200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr12:4931800-4932000	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links