Variant report

Variant	rs2480933
Chromosome Location	chr9:117864609-117864610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10982535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250019	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs1250021	0.95[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1250022	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1250026	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1250027	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1273108	0.84[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1330355	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1330356	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1511	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[ASN][1000 genomes]
rs1755639	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1755646	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1757106	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs1757107	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1819419	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1929395	0.95[JPT][hapmap]
rs2183701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274836	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[ASN][1000 genomes]
rs2480930	0.83[ASN][1000 genomes]
rs2480932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2482080	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2989518	0.82[JPT][hapmap]
rs2989519	0.81[ASW][hapmap]
rs3789867	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789868	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769331	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881496	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs944227	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2480933	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
2	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:117857400-117867400	Weak transcription	NHLF	lung
6	chr9:117857600-117866000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:117857600-117866800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:117858800-117865600	Enhancers	Rectal Smooth Muscle	rectum
9	chr9:117859400-117865800	Weak transcription	NHEK	skin
10	chr9:117859600-117865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:117861000-117868400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:117861600-117870400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:117861600-117876000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:117861800-117874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:117862400-117865200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:117862400-117872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:117862600-117865800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr9:117862600-117865800	Weak transcription	NHDF-Ad	bronchial
19	chr9:117862600-117867000	Weak transcription	NH-A	brain
20	chr9:117862600-117867600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
22	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
23	chr9:117862800-117865000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:117862800-117865400	Weak transcription	Osteobl	bone
25	chr9:117862800-117865600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:117863000-117865400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:117863600-117867400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:117863800-117864800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:117863800-117865000	Enhancers	Colon Smooth Muscle	Colon
30	chr9:117863800-117865600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:117864600-117867200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr9:117864600-117868200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:117864600-117870600	Enhancers	HMEC	breast

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