Variant report

Variant	rs1273108
Chromosome Location	chr9:117866424-117866425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10982535	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1250019	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs1250023	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1250026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250027	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs1330349	0.92[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs1330350	0.92[CEU][hapmap]
rs1330356	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1330360	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs1360291	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1511	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs1755639	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1757100	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1757107	0.82[JPT][hapmap]
rs1929395	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap]
rs2183701	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2274836	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs2480931	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2480932	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs2480933	0.84[CHD][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2482078	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2482080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2988578	0.92[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2989518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3789867	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs3789868	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap]
rs769331	0.82[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs881496	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs944227	0.82[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1273108	SLC31A2	cis	cerebellum	SCAN
rs1273108	SNX30	cis	cerebellum	SCAN
rs1273108	C9orf80	cis	cerebellum	SCAN

Chromatin state (count:34 , 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	chr9:117857600-117866800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:117861000-117868400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:117861600-117870400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:117861600-117876000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:117861800-117874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:117862400-117872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:117862600-117867000	Weak transcription	NH-A	brain
13	chr9:117862600-117867600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
15	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
16	chr9:117863600-117867400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:117864600-117867200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr9:117864600-117868200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:117864600-117870600	Enhancers	HMEC	breast
20	chr9:117864800-117866800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:117865400-117870000	Enhancers	Colon Smooth Muscle	Colon
22	chr9:117865600-117867000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:117865600-117867000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:117865600-117868000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:117865800-117867000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:117865800-117868200	Enhancers	NHDF-Ad	bronchial
27	chr9:117865800-117869000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr9:117865800-117870800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:117866000-117867000	Enhancers	Osteobl	bone
30	chr9:117866200-117866600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:117866200-117867400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:117866400-117866600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:117866400-117867000	Enhancers	NHEK	skin
34	chr9:117866400-117875000	Enhancers	Rectal Smooth Muscle	rectum

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