Variant report

Variant	rs1335330
Chromosome Location	chr9:117906101-117906102
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10982546	0.88[CEU][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13302198	0.83[EUR][1000 genomes]
rs1335342	0.86[EUR][1000 genomes]
rs1335343	0.81[EUR][1000 genomes]
rs1537721	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1537722	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537727	0.96[CEU][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1537728	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1591421	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs1855691	0.84[EUR][1000 genomes]
rs2094941	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2992148	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4246907	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4978618	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4978623	0.83[EUR][1000 genomes]
rs4979510	0.83[EUR][1000 genomes]
rs55991771	0.81[EUR][1000 genomes]
rs56394382	0.81[EUR][1000 genomes]
rs6478148	0.82[EUR][1000 genomes]
rs7030031	0.88[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs884789	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]

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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1335330	RGL4	trans	parietal	SCAN
rs1335330	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117890200-117909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:117900000-117908400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:117904000-117907400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:117904200-117907000	Enhancers	Brain Hippocampus Middle	brain
5	chr9:117904200-117909200	Weak transcription	Aorta	Aorta
6	chr9:117904800-117907600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:117904800-117910000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:117904800-117910200	Enhancers	NHDF-Ad	bronchial
9	chr9:117905000-117907800	Enhancers	Dnd41	blood
10	chr9:117905000-117910000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:117905000-117910200	Enhancers	Osteobl	bone
12	chr9:117905400-117907000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:117905400-117908000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:117905400-117908200	Weak transcription	NHLF	lung
15	chr9:117905600-117906800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:117905600-117908400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:117906000-117908400	Weak transcription	HSMM	muscle
18	chr9:117906000-117909200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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