Variant report

Variant	rs12379253
Chromosome Location	chr9:72512216-72512217
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11140716	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11140750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140836	1.00[CHD][hapmap]
rs11140842	1.00[CHD][hapmap]
rs12378305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap]
rs13283032	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284442	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13295978	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871283	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34702508	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35822389	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022971	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7038189	0.90[EUR][1000 genomes]
rs7469302	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766002	0.88[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852049	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv466416	chr9:72479046-72513240	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv614581	chr9:72479046-72513240	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv893439	chr9:72500956-72568962	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12379253	C9orf135	cis	parietal	SCAN
rs12379253	PTAR1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72500800-72512800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:72501200-72512600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:72501800-72513000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:72502800-72512600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:72502800-72512600	Weak transcription	HMEC	breast
6	chr9:72508200-72512600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:72508200-72512600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:72508600-72512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:72508800-72512600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:72509000-72512600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:72509000-72512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:72509800-72512400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:72509800-72512600	Weak transcription	NHDF-Ad	bronchial
14	chr9:72509800-72512800	Weak transcription	NHLF	lung
15	chr9:72509800-72513000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:72509800-72514000	Weak transcription	Brain Anterior Caudate	brain
17	chr9:72510200-72512400	Weak transcription	A549	lung
18	chr9:72510200-72512400	Weak transcription	Osteobl	bone
19	chr9:72510200-72512600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr9:72510200-72513400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:72510400-72512600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:72510600-72512800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:72511800-72514600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:72512000-72515800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links