Variant report

Variant	rs1020963
Chromosome Location	chr9:97789745-97789746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97785037..97786966-chr9:97789243..97791413,3	MCF-7	breast:
2	chr9:97783764..97786051-chr9:97788470..97790440,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1004373	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10117370	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10119512	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10121760	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10123819	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512253	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10761364	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761366	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10761368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761369	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10761372	0.95[ASN][1000 genomes]
rs10821433	0.89[JPT][hapmap]
rs10993427	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10993456	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs10993464	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10993467	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1113102	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12339639	0.90[JPT][hapmap];0.82[TSI][hapmap]
rs12346261	0.90[JPT][hapmap]
rs1412488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564234	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1571894	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1571895	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][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];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2061800	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2404302	0.90[CEU][hapmap];0.94[CHB][hapmap]
rs2404305	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2404456	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs3802454	0.90[CEU][hapmap];0.94[CHB][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3802456	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4537362	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4743979	0.90[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743980	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743981	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743982	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4743984	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744423	0.81[CEU][hapmap];0.94[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744424	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744425	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4744426	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744428	0.84[AMR][1000 genomes]
rs4744430	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744431	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744432	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744433	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744435	0.81[EUR][1000 genomes]
rs4744436	0.81[CEU][hapmap]
rs6479588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479591	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6479592	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7020709	0.80[EUR][1000 genomes]
rs7021351	1.00[ASW][hapmap];0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7022452	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7023719	0.81[CHB][hapmap]
rs7043705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7048786	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7048941	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7851173	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7857679	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7862156	0.81[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7863291	0.90[CEU][hapmap];0.82[CHB][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7865144	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871218	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7873479	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873567	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs962229	0.82[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1020963	OGN	cis	parietal	SCAN
rs1020963	FOXE1	cis	parietal	SCAN
rs1020963	hCG_2003663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97769600-97790200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97773200-97793200	Weak transcription	Brain Germinal Matrix	brain
4	chr9:97777400-97794200	Weak transcription	Thymus	Thymus
5	chr9:97780600-97790800	Weak transcription	Fetal Brain Female	brain
6	chr9:97781200-97793600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:97781400-97793200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:97781400-97793600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:97782000-97792800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr9:97782600-97793600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr9:97783600-97794000	Weak transcription	GM12878-XiMat	blood
12	chr9:97786200-97790600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:97786200-97791800	Enhancers	Right Ventricle	heart
14	chr9:97786400-97790200	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr9:97787000-97790200	Weak transcription	HMEC	breast
16	chr9:97787000-97794000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr9:97787600-97793000	Genic enhancers	HepG2	liver
18	chr9:97787800-97790200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:97787800-97790200	Weak transcription	Gastric	stomach
20	chr9:97787800-97792800	Weak transcription	Spleen	Spleen
21	chr9:97787800-97793800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:97787800-97795800	Genic enhancers	Osteobl	bone
23	chr9:97788000-97790200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:97788000-97790200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:97788000-97791200	Weak transcription	Colonic Mucosa	Colon
26	chr9:97788000-97794800	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr9:97788200-97790200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:97788200-97790200	Weak transcription	Fetal Muscle Leg	muscle
29	chr9:97788200-97790200	Weak transcription	Left Ventricle	heart
30	chr9:97788200-97790200	Weak transcription	Lung	lung
31	chr9:97788200-97790200	Weak transcription	Pancreas	Pancrea
32	chr9:97788200-97790200	Weak transcription	Right Atrium	heart
33	chr9:97788200-97790600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:97788200-97790600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:97788200-97790600	Weak transcription	Ovary	ovary
36	chr9:97788200-97791000	Weak transcription	Hela-S3	cervix
37	chr9:97788200-97791200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:97788200-97792800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:97788200-97793000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr9:97788200-97794400	Weak transcription	K562	blood
41	chr9:97788400-97790200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:97788400-97790200	Weak transcription	Esophagus	oesophagus
43	chr9:97788400-97791200	Weak transcription	Placenta	Placenta
44	chr9:97788400-97791200	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:97788400-97795800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr9:97788600-97791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:97788600-97791200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr9:97788800-97789800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:97788800-97790000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:97788800-97790000	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links