Variant report

Variant	rs10992382
Chromosome Location	chr9:95361063-95361064
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr9:95360661-95361097	HepG2	liver:	n/a	n/a
2	FOXA1	chr9:95360576-95361081	HepG2	liver:	n/a	n/a
3	MAX	chr9:95360589-95361145	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:95321743..95324130-chr9:95360863..95362407,2	MCF-7	breast:
2	chr9:95357901..95361208-chr9:95361655..95366316,4	K562	blood:
3	chr9:95360478..95362522-chr9:95373991..95376021,2	MCF-7	breast:
4	chr9:95355167..95358650-chr9:95359849..95362107,3	K562	blood:
5	chr9:95354681..95356667-chr9:95358553..95361349,2	K562	blood:

No data

Variant related genes	Relation type
CENPP	TF binding region
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10491806	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10820997	0.83[ASW][hapmap];0.84[MEX][hapmap]
rs10820998	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs10821009	0.84[MEX][hapmap]
rs10821012	0.83[MEX][hapmap]
rs10992367	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs10992380	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.92[ASN][1000 genomes]
rs10992384	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10992390	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10992392	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10992394	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10992404	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10992406	0.83[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs10992407	0.88[CHB][hapmap]
rs10992408	0.94[CHB][hapmap];0.93[YRI][hapmap]
rs10992409	0.84[AFR][1000 genomes]
rs10992414	0.88[CHB][hapmap]
rs10992426	0.85[AMR][1000 genomes]
rs10992433	0.85[AMR][1000 genomes]
rs10992434	0.84[MEX][hapmap]
rs10992444	0.84[MEX][hapmap]
rs10992445	0.84[MEX][hapmap]
rs10992448	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992453	0.88[CHB][hapmap]
rs10992460	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs10992461	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs1117670	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12236013	0.81[AMR][1000 genomes]
rs12236754	0.82[CEU][hapmap];0.87[CHB][hapmap]
rs12237216	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12238691	0.88[CHB][hapmap]
rs12685080	0.81[YRI][hapmap]
rs12685257	0.84[MEX][hapmap]
rs12685780	0.84[MEX][hapmap]
rs12686780	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12686781	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1323523	0.91[CEU][hapmap];0.88[CHB][hapmap];0.81[AMR][1000 genomes]
rs1326775	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1407944	0.88[AMR][1000 genomes]
rs1552908	0.80[JPT][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1575460	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17366488	0.81[AMR][1000 genomes]
rs1853468	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1874128	0.83[ASW][hapmap];0.83[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980705	0.84[MEX][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2038685	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2038686	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088054	0.81[ASN][1000 genomes]
rs2088055	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131919	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs2146848	0.91[CEU][hapmap]
rs2148537	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2172716	0.81[ASN][1000 genomes]
rs2181584	0.88[CHB][hapmap]
rs2274413	0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2277166	0.83[AMR][1000 genomes]
rs2281888	0.84[MEX][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2296080	0.84[MEX][hapmap]
rs3203916	0.84[MEX][hapmap]
rs3739605	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs41266683	0.84[AMR][1000 genomes]
rs556	0.83[MEX][hapmap]
rs58045868	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6479426	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7031163	0.88[CHB][hapmap];0.96[MEX][hapmap]
rs7850871	0.83[AMR][1000 genomes]
rs7851947	0.88[AMR][1000 genomes]
rs7853617	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7856147	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs7857105	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7857502	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes]
rs7863882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7863890	0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs7864889	0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs7875050	0.90[CEU][hapmap];0.94[CHB][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs879812	0.84[MEX][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs912261	0.91[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs912264	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs971984	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9775970	0.82[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10992382	ANKRD19	cis	cerebellum	SCAN
rs10992382	C9orf89	cis	cerebellum	SCAN
rs10992382	BICD2	Cis_1M	lymphoblastoid	RTeQTL
rs10992382	CENPP	cis	multi-tissue	Pritchard
rs10992382	FBP1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95347600-95365800	Weak transcription	Thymus	Thymus
2	chr9:95347800-95364000	Weak transcription	Left Ventricle	heart
3	chr9:95353000-95362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:95354000-95362200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:95355600-95362000	Weak transcription	Aorta	Aorta
6	chr9:95355600-95362800	Weak transcription	Right Ventricle	heart
7	chr9:95355800-95367000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:95356200-95362600	Weak transcription	Fetal Thymus	thymus
9	chr9:95356400-95362000	Weak transcription	HSMMtube	muscle
10	chr9:95356400-95362400	Weak transcription	HSMM	muscle
11	chr9:95359200-95362600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:95359600-95363200	Weak transcription	Fetal Kidney	kidney
13	chr9:95360000-95364000	Enhancers	HepG2	liver
14	chr9:95360200-95370200	Weak transcription	Fetal Heart	heart
15	chr9:95360400-95361400	Enhancers	Right Atrium	heart
16	chr9:95360400-95362000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:95360400-95362200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:95360400-95362400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr9:95360400-95366000	Enhancers	Fetal Muscle Trunk	muscle
20	chr9:95360400-95366000	Enhancers	Fetal Muscle Leg	muscle
21	chr9:95360600-95361600	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:95360600-95362000	Weak transcription	NHEK	skin
23	chr9:95360600-95362600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:95360600-95362600	Enhancers	Adipose Nuclei	Adipose
25	chr9:95360600-95362800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr9:95360600-95363000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:95360800-95361400	Weak transcription	Fetal Stomach	stomach
28	chr9:95360800-95362000	Weak transcription	Fetal Lung	lung
29	chr9:95360800-95362200	Weak transcription	Esophagus	oesophagus
30	chr9:95360800-95362200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:95360800-95362200	Weak transcription	Fetal Intestine Small	intestine
32	chr9:95360800-95362200	Weak transcription	Placenta	Placenta
33	chr9:95360800-95362200	Weak transcription	Lung	lung
34	chr9:95360800-95363200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr9:95361000-95362000	Weak transcription	NHDF-Ad	bronchial
36	chr9:95361000-95362200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:95361000-95362200	Enhancers	Stomach Smooth Muscle	stomach
38	chr9:95361000-95362400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:95361000-95362800	Weak transcription	Ovary	ovary
40	chr9:95361000-95362800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links