Variant report

Variant	rs1360291
Chromosome Location	chr9:117870230-117870231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117870174..117872468-chr9:117872679..117875329,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000041982	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1061494	0.80[JPT][hapmap]
rs1250023	0.94[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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1250026	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1271449	0.85[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.82[MKK][hapmap]
rs1272041	0.80[JPT][hapmap]
rs1273108	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]
rs1330349	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1330350	0.88[CEU][hapmap]
rs1330360	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1617917	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1755638	0.80[JPT][hapmap]
rs1755640	0.86[JPT][hapmap]
rs1757096	0.80[JPT][hapmap]
rs1757100	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];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1757108	0.83[JPT][hapmap]
rs1888220	0.80[JPT][hapmap]
rs1929395	0.88[CEU][hapmap]
rs2480931	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2482077	0.80[JPT][hapmap]
rs2482078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2482080	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2988578	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2989518	0.96[CEU][hapmap]
rs2989519	0.80[JPT][hapmap]
rs2992147	0.80[JPT][hapmap]
rs944510	0.80[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1360291	C9orf80	cis	cerebellum	SCAN
rs1360291	SLC31A2	cis	cerebellum	SCAN
rs1360291	ATP6V1G1	cis	cerebellum	SCAN
rs1360291	SNX30	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	chr9:117853400-117874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:117861600-117870400	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr9:117861600-117876000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:117861800-117874800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:117862400-117872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:117862600-117877200	Weak transcription	Fetal Kidney	kidney
9	chr9:117862600-117877200	Weak transcription	Fetal Stomach	stomach
10	chr9:117864600-117870600	Enhancers	HMEC	breast
11	chr9:117865800-117870800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr9:117866400-117875000	Enhancers	Rectal Smooth Muscle	rectum
13	chr9:117866600-117870800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:117866800-117870400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:117867000-117870400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:117867000-117870400	Enhancers	NH-A	brain
17	chr9:117867400-117870800	Enhancers	Liver	Liver
18	chr9:117867400-117872200	Enhancers	NHEK	skin
19	chr9:117867400-117874000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:117868400-117870400	Enhancers	Osteobl	bone
21	chr9:117868800-117871600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:117869000-117876800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:117869000-117876800	Weak transcription	HSMM	muscle
24	chr9:117869200-117870400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:117869200-117870800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:117869200-117871000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:117869200-117872200	Enhancers	NHDF-Ad	bronchial
28	chr9:117869200-117878400	Weak transcription	Fetal Lung	lung
29	chr9:117869400-117870400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:117869800-117872800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:117870000-117870600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:117870000-117872400	Genic enhancers	Colon Smooth Muscle	Colon
33	chr9:117870200-117870400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:117870200-117870400	Enhancers	Esophagus	oesophagus
35	chr9:117870200-117870400	Enhancers	Stomach Mucosa	stomach
36	chr9:117870200-117870400	Genic enhancers	NHLF	lung
37	chr9:117870200-117870600	Enhancers	Stomach Smooth Muscle	stomach
38	chr9:117870200-117871600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:117870200-117876000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr9:117870200-117876600	Genic enhancers	Cortex derived primary cultured neurospheres	brain

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