Variant report

Variant	rs3789867
Chromosome Location	chr9:117875688-117875689
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:117858058-117881674	U87	brain:	n/a	n/a
2	POLR2A	chr9:117875560-117876095	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr9:117874002-117876957	IMR90	lung:	n/a	n/a
4	POLR2A	chr9:117875288-117875717	U87	brain:	n/a	n/a
5	POLR2A	chr9:117863693-117881740	U87	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1061494	0.82[GIH][hapmap]
rs10982535	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1250019	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1250021	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1250022	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1250026	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1250027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1273108	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs1330351	0.82[TSI][hapmap]
rs1330355	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1330356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1511	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1755639	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1755646	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1757096	0.82[GIH][hapmap]
rs1757106	0.96[CEU][hapmap];0.94[JPT][hapmap]
rs1757107	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1819419	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1929395	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2183701	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274836	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.89[ASN][1000 genomes]
rs2480930	0.85[ASN][1000 genomes]
rs2480932	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2480933	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]
rs2482077	0.82[GIH][hapmap]
rs2482080	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2989518	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2989519	0.82[GIH][hapmap]
rs2992147	0.82[GIH][hapmap]
rs3789868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979493	0.80[EUR][1000 genomes]
rs769331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs881496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs944227	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs944510	0.82[GIH][hapmap]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789867	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:40 , 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	chr9:117861600-117876000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
5	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
6	chr9:117869000-117876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr9:117869000-117876800	Weak transcription	HSMM	muscle
8	chr9:117869200-117878400	Weak transcription	Fetal Lung	lung
9	chr9:117870200-117876000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr9:117870200-117876600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:117870400-117876600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:117870400-117876600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:117870400-117879000	Weak transcription	Esophagus	oesophagus
14	chr9:117872000-117876600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:117872200-117876400	Weak transcription	HMEC	breast
16	chr9:117873800-117875800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:117873800-117876200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:117874000-117876400	Strong transcription	NHEK	skin
19	chr9:117874000-117876600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr9:117874000-117876800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:117874000-117876800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr9:117874000-117877000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr9:117874200-117875800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr9:117874400-117876200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:117874400-117876800	Strong transcription	NHDF-Ad	bronchial
26	chr9:117874600-117876600	Strong transcription	NH-A	brain
27	chr9:117874600-117877600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr9:117874800-117876400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr9:117874800-117876600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:117875000-117876000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:117875000-117876600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:117875000-117876800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:117875000-117876800	Strong transcription	NHLF	lung
34	chr9:117875400-117875800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:117875400-117875800	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
36	chr9:117875400-117876000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr9:117875400-117876000	Enhancers	Rectal Smooth Muscle	rectum
38	chr9:117875400-117876400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:117875400-117879000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:117875600-117877000	Genic enhancers	Osteobl	bone

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