Variant report

Variant	rs1537722
Chromosome Location	chr9:117896349-117896350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10982546	0.88[CEU][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1273108	0.81[CHD][hapmap]
rs13302198	0.83[EUR][1000 genomes]
rs1335330	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335342	0.86[EUR][1000 genomes]
rs1335343	0.81[EUR][1000 genomes]
rs1537721	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1537727	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1537728	0.86[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[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];0.84[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2992148	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4246907	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4978618	0.97[AMR][1000 genomes];0.96[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];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs884789	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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
5	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
rs1537722	C9orf80	cis	cerebellum	SCAN
rs1537722	RGL4	trans	parietal	SCAN

Chromatin state (count:22 , 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	chr9:117894200-117898800	Enhancers	Fetal Stomach	stomach
3	chr9:117894400-117896600	Enhancers	NH-A	brain
4	chr9:117894800-117899200	Enhancers	NHDF-Ad	bronchial
5	chr9:117895200-117896800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:117895200-117898200	Weak transcription	Esophagus	oesophagus
7	chr9:117895200-117898800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:117895200-117899400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:117895400-117897200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:117895400-117897600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:117895400-117897600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:117895400-117897800	Enhancers	Osteobl	bone
13	chr9:117895400-117900000	Enhancers	NHLF	lung
14	chr9:117895400-117903200	Weak transcription	Fetal Kidney	kidney
15	chr9:117895600-117897400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:117895800-117896600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:117896000-117896400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:117896200-117896600	Enhancers	Dnd41	blood
19	chr9:117896200-117896800	Weak transcription	Fetal Lung	lung
20	chr9:117896200-117897000	Weak transcription	Fetal Muscle Leg	muscle
21	chr9:117896200-117899200	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:117896200-117899800	Enhancers	Colon Smooth Muscle	Colon

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