Variant report

Variant	rs6586
Chromosome Location	chr9:100666931-100666932
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	chr9:100665233..100671095-chr9:100679720..100686341,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10113907	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10818239	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10984193	0.90[YRI][hapmap]
rs11999801	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12003789	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13300874	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13301569	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1443434	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs1443435	0.81[CHB][hapmap];0.84[GIH][hapmap]
rs1561958	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1561959	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867278	0.84[GIH][hapmap]
rs2120263	0.88[CHB][hapmap];0.81[AMR][1000 genomes]
rs2282192	0.88[CHB][hapmap]
rs2417577	0.81[CHB][hapmap]
rs3183927	0.81[CHB][hapmap]
rs3758249	0.81[CHB][hapmap]
rs3758251	0.81[CHB][hapmap]
rs3758253	0.81[CHB][hapmap]
rs3758254	0.81[CHB][hapmap]
rs3780420	0.81[CHB][hapmap]
rs4631576	0.81[CHB][hapmap]
rs4743140	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4743147	0.84[CHB][hapmap]
rs6478450	0.86[EUR][1000 genomes]
rs67449879	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7020644	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033315	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7357707	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7853349	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7870125	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs874004	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs894673	0.81[CHB][hapmap]
rs907577	0.81[CHB][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1048135	chr9:100666931-100717030	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6586	C9orf156	cis	Frontal Cortex	GTEx
rs6586	C9orf156	cis	Temporal Cortex	GTEx
rs6586	C9orf156	cis	Skin Sun Exposed Lower leg	GTEx
rs6586	GALNT12	cis	cerebellum	SCAN
rs6586	C9orf156	cis	Brain Pons	GTEx
rs6586	C9orf156	cis	Esophagus Muscularis	GTEx
rs6586	C9orf156	cis	parietal	SCAN
rs6586	C9orf156	cis	Esophagus Mucosa	GTEx
rs6586	C9orf156	cis	Thyroid	GTEx
rs6586	C9orf156	cis	cerebellum	SCAN
rs6586	C9orf156	cis	multi-tissue	Pritchard
rs6586	FOXE1	cis	Esophagus Mucosa	GTEx
rs6586	C9orf156	cis	Cerebellum	GTEx
rs6586	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100653000-100667000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100656000-100667600	Weak transcription	Fetal Muscle Leg	muscle
3	chr9:100656000-100669400	Weak transcription	Brain Substantia Nigra	brain
4	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:100656400-100668400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:100656400-100669800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:100656400-100669800	Weak transcription	Fetal Brain Female	brain
8	chr9:100656600-100667000	Weak transcription	Brain Anterior Caudate	brain
9	chr9:100656800-100668400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:100656800-100669400	Weak transcription	Left Ventricle	heart
11	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
12	chr9:100657000-100669400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:100657000-100669400	Weak transcription	Right Ventricle	heart
14	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr9:100658400-100669400	Weak transcription	Hela-S3	cervix
16	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:100658600-100667600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:100658600-100669400	Weak transcription	Gastric	stomach
19	chr9:100658600-100671600	Weak transcription	Ovary	ovary
20	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
21	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
22	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:100660200-100671200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:100660600-100668400	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:100660800-100669400	Weak transcription	Aorta	Aorta
26	chr9:100661200-100669800	Weak transcription	K562	blood
27	chr9:100662000-100667400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr9:100662400-100667200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr9:100662800-100667000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:100662800-100669400	Weak transcription	Lung	lung
31	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:100663000-100667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:100663000-100667000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:100663000-100668400	Weak transcription	Spleen	Spleen
35	chr9:100663000-100669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:100663000-100672200	Weak transcription	Colonic Mucosa	Colon
37	chr9:100663200-100667000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:100663200-100671600	Weak transcription	HSMMtube	muscle
39	chr9:100663200-100671800	Weak transcription	NH-A	brain
40	chr9:100663200-100672000	Weak transcription	HepG2	liver
41	chr9:100663200-100672200	Weak transcription	HSMM	muscle
42	chr9:100663400-100667400	Weak transcription	Osteobl	bone
43	chr9:100663400-100667600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr9:100663400-100670200	Weak transcription	NHLF	lung
45	chr9:100663400-100671200	Weak transcription	Brain Angular Gyrus	brain
46	chr9:100663400-100671600	Weak transcription	NHDF-Ad	bronchial
47	chr9:100663400-100672600	Weak transcription	A549	lung
48	chr9:100663600-100667000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:100663600-100671000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:100663800-100667000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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