Variant report

Variant	rs10992367
Chromosome Location	chr9:95323135-95323136
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	chr9:95321743..95324130-chr9:95360863..95362407,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10491806	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10761156	1.00[YRI][hapmap]
rs10820997	0.84[MEX][hapmap]
rs10820998	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs10821001	0.84[AMR][1000 genomes]
rs10821003	0.84[AMR][1000 genomes]
rs10821004	0.84[AMR][1000 genomes]
rs10821005	0.84[AMR][1000 genomes]
rs10821009	0.84[MEX][hapmap]
rs10821011	0.83[AMR][1000 genomes]
rs10821012	0.84[MEX][hapmap]
rs10821014	0.84[AMR][1000 genomes]
rs10992380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992382	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]
rs10992384	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10992390	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[AMR][1000 genomes]
rs10992392	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes]
rs10992396	0.85[AMR][1000 genomes]
rs10992406	0.88[CHB][hapmap]
rs10992407	0.82[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs10992408	0.88[CHB][hapmap];0.80[AMR][1000 genomes]
rs10992409	0.80[AMR][1000 genomes]
rs10992412	0.85[AMR][1000 genomes]
rs10992414	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs10992416	0.84[AMR][1000 genomes]
rs10992417	0.84[AMR][1000 genomes]
rs10992420	0.84[AMR][1000 genomes]
rs10992422	0.84[AMR][1000 genomes]
rs10992423	0.84[AMR][1000 genomes]
rs10992434	0.84[MEX][hapmap]
rs10992437	0.84[AMR][1000 genomes]
rs10992444	0.84[MEX][hapmap]
rs10992445	0.84[MEX][hapmap]
rs10992447	0.89[TSI][hapmap]
rs10992448	0.82[CHB][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs1117670	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs1152759	1.00[YRI][hapmap]
rs11533010	0.84[AMR][1000 genomes]
rs12236013	0.90[AMR][1000 genomes]
rs12236754	0.81[CHB][hapmap]
rs12238691	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs12685257	0.84[MEX][hapmap]
rs12685358	0.84[AMR][1000 genomes]
rs12686771	0.89[TSI][hapmap]
rs12686780	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12686781	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1323523	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1326775	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1552908	0.80[JPT][hapmap];0.84[MEX][hapmap]
rs1575460	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17366488	0.90[AMR][1000 genomes]
rs1853468	0.91[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1980705	0.84[MEX][hapmap]
rs2025389	1.00[YRI][hapmap]
rs2031262	1.00[YRI][hapmap]
rs2038685	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2088054	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2131919	1.00[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];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2146848	0.91[CEU][hapmap]
rs2148537	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2172716	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2181584	0.82[CHB][hapmap];0.84[AMR][1000 genomes]
rs2281888	0.84[MEX][hapmap]
rs2296080	0.84[MEX][hapmap]
rs230222	1.00[YRI][hapmap]
rs3203916	0.84[MEX][hapmap]
rs331380	1.00[YRI][hapmap]
rs3739605	0.82[CHB][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs556	0.84[MEX][hapmap]
rs58952648	0.84[AMR][1000 genomes]
rs60498616	0.84[AMR][1000 genomes]
rs6479426	0.83[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.80[ASN][1000 genomes]
rs67601697	0.87[AMR][1000 genomes]
rs753804	0.84[AMR][1000 genomes]
rs754600	0.88[AMR][1000 genomes]
rs7853617	0.84[AMR][1000 genomes]
rs7856147	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7857105	0.91[CEU][hapmap];0.88[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes]
rs7857502	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs7863882	0.83[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs7863890	0.84[MEX][hapmap]
rs7869603	0.84[AMR][1000 genomes]
rs7875050	0.89[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes]
rs879812	0.84[MEX][hapmap]
rs912261	0.88[CHB][hapmap];1.00[MEX][hapmap]
rs912264	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs971984	1.00[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10992367	ASPN	cis	cerebellum	SCAN
rs10992367	ANKRD19	cis	cerebellum	SCAN
rs10992367	FBP1	cis	cerebellum	SCAN
rs10992367	IARS	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95308600-95324000	Weak transcription	Fetal Intestine Small	intestine
2	chr9:95310800-95323600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:95320600-95324200	Weak transcription	Small Intestine	intestine
4	chr9:95321200-95323400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:95321200-95325400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:95321400-95324000	Weak transcription	Esophagus	oesophagus
7	chr9:95321600-95323400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:95321600-95323400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:95321600-95325400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:95321800-95326400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:95322000-95324200	Weak transcription	Adipose Nuclei	Adipose
12	chr9:95323000-95323400	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links