Variant report

Variant	rs1561961
Chromosome Location	chr9:100667599-100667600
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: 97 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1007506	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs10113884	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10115216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117642	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119760	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10119853	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10120412	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10122541	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10123699	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10512255	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739526	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759975	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759981	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10760011	0.84[AMR][1000 genomes]
rs10818175	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818213	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818241	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10984079	0.83[ASN][1000 genomes]
rs10984103	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10984134	0.83[ASN][1000 genomes]
rs10984156	0.83[ASN][1000 genomes]
rs10984195	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984218	0.87[ASN][1000 genomes]
rs10984222	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs10984230	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984235	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10984253	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10984311	0.88[CHB][hapmap]
rs10984424	0.82[CHB][hapmap]
rs12004762	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343182	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12347191	0.81[EUR][1000 genomes]
rs12550872	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286291	0.83[EUR][1000 genomes]
rs13287360	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13299924	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1443434	0.85[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs1443435	0.85[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs1443436	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1561957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867278	0.88[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap]
rs1955143	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1955144	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955145	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2120264	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282190	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417575	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2417576	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28417086	0.87[ASN][1000 genomes]
rs28697997	0.87[ASN][1000 genomes]
rs28703314	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3021525	0.85[ASN][1000 genomes]
rs35324451	0.82[EUR][1000 genomes]
rs3758249	0.85[CEU][hapmap]
rs3758250	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs3758251	0.85[CEU][hapmap]
rs3808893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808895	0.90[CHB][hapmap]
rs3824495	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255258	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4460498	0.81[EUR][1000 genomes]
rs4743139	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743142	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6478445	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6478469	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478471	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022148	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027221	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7031386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032086	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7032114	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034249	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034336	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7034648	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7037175	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7037324	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038998	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044121	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044799	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048255	1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72753537	0.91[ASN][1000 genomes]
rs7860144	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7866436	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868534	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs894673	0.85[CEU][hapmap]
rs907577	0.85[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap]
rs907581	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs925487	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9299258	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9775370	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs993501	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1561961	C9orf156	cis	cerebellum	SCAN
rs1561961	TSTD2	cis	parietal	SCAN
rs1561961	C9orf156	cis	Frontal Cortex	GTEx
rs1561961	C9orf156	cis	Temporal Cortex	GTEx
rs1561961	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	chr9:100656000-100667600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:100656000-100669400	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100656200-100670400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:100656400-100668400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:100656400-100669800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:100656400-100669800	Weak transcription	Fetal Brain Female	brain
7	chr9:100656800-100668400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:100656800-100669400	Weak transcription	Left Ventricle	heart
9	chr9:100656800-100672400	Weak transcription	Stomach Mucosa	stomach
10	chr9:100657000-100669400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:100657000-100669400	Weak transcription	Right Ventricle	heart
12	chr9:100658200-100671600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:100658400-100669400	Weak transcription	Hela-S3	cervix
14	chr9:100658400-100671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:100658600-100667600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:100658600-100669400	Weak transcription	Gastric	stomach
17	chr9:100658600-100671600	Weak transcription	Ovary	ovary
18	chr9:100658600-100671600	Weak transcription	Small Intestine	intestine
19	chr9:100658600-100672200	Weak transcription	Esophagus	oesophagus
20	chr9:100658800-100681800	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr9:100660200-100671200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr9:100660600-100668400	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:100660800-100669400	Weak transcription	Aorta	Aorta
24	chr9:100661200-100669800	Weak transcription	K562	blood
25	chr9:100662800-100669400	Weak transcription	Lung	lung
26	chr9:100662800-100684200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:100663000-100668400	Weak transcription	Spleen	Spleen
28	chr9:100663000-100669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:100663000-100672200	Weak transcription	Colonic Mucosa	Colon
30	chr9:100663200-100671600	Weak transcription	HSMMtube	muscle
31	chr9:100663200-100671800	Weak transcription	NH-A	brain
32	chr9:100663200-100672000	Weak transcription	HepG2	liver
33	chr9:100663200-100672200	Weak transcription	HSMM	muscle
34	chr9:100663400-100667600	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr9:100663400-100670200	Weak transcription	NHLF	lung
36	chr9:100663400-100671200	Weak transcription	Brain Angular Gyrus	brain
37	chr9:100663400-100671600	Weak transcription	NHDF-Ad	bronchial
38	chr9:100663400-100672600	Weak transcription	A549	lung
39	chr9:100663600-100671000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:100663800-100669400	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:100664000-100673200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:100664400-100668200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:100664400-100672200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:100664600-100668400	Weak transcription	HUVEC	blood vessel
45	chr9:100665200-100667800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:100665400-100667800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr9:100665400-100671600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:100665400-100679000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:100665600-100671000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:100665600-100671600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links