Variant report

Variant	rs1250019
Chromosome Location	chr9:117856318-117856319
allele	A/G
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	JUND	chr9:117856283-117856506	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:117853634-117857758	U87	brain:	n/a	n/a
3	POLR2A	chr9:117851943-117857764	U87	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1061494	0.87[GIH][hapmap]
rs10982535	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1250021	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs1250022	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1250026	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1250027	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1273108	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs1330351	0.84[TSI][hapmap]
rs1330355	0.86[ASN][1000 genomes]
rs1330356	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1511	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1755646	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1757096	0.87[GIH][hapmap]
rs1757106	1.00[CEU][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1757107	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1929395	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2183701	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2274836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2480930	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2480932	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2480933	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]
rs2482077	0.87[GIH][hapmap]
rs2482080	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2989518	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2989519	0.87[GIH][hapmap]
rs2992147	0.87[GIH][hapmap]
rs3789867	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]
rs3789868	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]
rs4979493	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs769331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs881496	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs944227	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs944510	0.87[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1250019	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117841200-117860600	Weak transcription	Fetal Kidney	kidney
3	chr9:117849000-117856400	Weak transcription	Brain Substantia Nigra	brain
4	chr9:117849400-117856800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:117849400-117876200	Weak transcription	Aorta	Aorta
6	chr9:117849400-117877600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:117849600-117856400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr9:117849600-117857000	Weak transcription	Spleen	Spleen
9	chr9:117849600-117864600	Weak transcription	HMEC	breast
10	chr9:117849800-117860400	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:117849800-117860600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:117850800-117857000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:117851200-117867200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:117852400-117857000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:117853200-117856600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:117853400-117857000	Weak transcription	NHLF	lung
17	chr9:117853400-117857200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:117853400-117857200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr9:117853400-117858800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr9:117853400-117861200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:117854000-117860600	Weak transcription	NHDF-Ad	bronchial
23	chr9:117854400-117860600	Weak transcription	Osteobl	bone
24	chr9:117855000-117857000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr9:117855200-117857000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:117855200-117857200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:117855200-117857600	Enhancers	Rectal Smooth Muscle	rectum
28	chr9:117855200-117861000	Weak transcription	NH-A	brain
29	chr9:117855400-117857200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr9:117855400-117857400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr9:117855400-117857600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:117855600-117856800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr9:117855600-117857200	Enhancers	Fetal Lung	lung
34	chr9:117855600-117857600	Enhancers	Colon Smooth Muscle	Colon
35	chr9:117855800-117856600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr9:117855800-117856600	Enhancers	Stomach Smooth Muscle	stomach
37	chr9:117855800-117856600	Strong transcription	NHEK	skin
38	chr9:117855800-117857200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr9:117856000-117856400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr9:117856000-117856600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr9:117856000-117856800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:117856000-117856800	Enhancers	Fetal Stomach	stomach
43	chr9:117856200-117856800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr9:117856200-117857200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:117856200-117857400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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