Variant report

Variant	rs10867929
Chromosome Location	chr9:85643603-85643604
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	chr9:85642474..85644010-chr9:85654073..85656615,2	MCF-7	breast:
2	chr9:85642708..85644228-chr9:85676845..85678578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165105	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1008171	0.88[CEU][hapmap]
rs1010480	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10115768	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10116216	0.81[CEU][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10116254	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10121156	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10121204	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10121395	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10126033	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10735559	0.89[CEU][hapmap]
rs10746694	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10780561	0.91[CEU][hapmap]
rs10780562	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10780563	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10780565	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10780567	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10867924	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10867925	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10867926	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10867927	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10867928	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1125915	0.81[CEU][hapmap]
rs13302349	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1393562	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1393563	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs1393564	0.92[CEU][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1393565	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs1502682	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1502683	0.89[CEU][hapmap]
rs1502684	0.89[CEU][hapmap]
rs1502685	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546315	1.00[CEU][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1546316	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1546317	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1580881	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1976455	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1995423	0.80[MEX][hapmap]
rs2062761	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs2279814	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs29001503	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4146960	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4146961	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4301515	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4348583	0.96[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4355855	0.89[CEU][hapmap]
rs4385545	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4391505	0.89[CEU][hapmap]
rs4460464	0.81[CEU][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4623517	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4628323	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4877244	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4877725	0.89[CEU][hapmap]
rs6559694	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6559695	0.96[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7019227	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7024864	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7029133	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043325	0.81[EUR][1000 genomes]
rs7045914	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7847666	1.00[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs7854101	1.00[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7866666	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7867614	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs871512	0.80[MEX][hapmap]
rs952450	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs998119	0.85[AMR][1000 genomes];0.89[EUR][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	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10867929	WNT10B	trans	cerebellum	SCAN
rs10867929	AGTPBP1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85603200-85643800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr9:85617200-85645800	Weak transcription	Stomach Mucosa	stomach
3	chr9:85621000-85645400	Weak transcription	Gastric	stomach
4	chr9:85639800-85645000	Enhancers	HMEC	breast
5	chr9:85640400-85644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:85640400-85656400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:85641400-85644800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:85641400-85645000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:85641400-85645000	Enhancers	NHEK	skin
10	chr9:85641600-85644400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:85642000-85643800	Weak transcription	Pancreas	Pancrea
12	chr9:85642400-85645400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:85643000-85644000	Weak transcription	Placenta	Placenta
14	chr9:85643000-85645000	Enhancers	A549	lung
15	chr9:85643200-85644200	Enhancers	Fetal Intestine Small	intestine
16	chr9:85643200-85645400	Weak transcription	Osteobl	bone
17	chr9:85643200-85645600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:85643200-85645600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr9:85643400-85644200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr9:85643400-85644800	Enhancers	Fetal Intestine Large	intestine
21	chr9:85643400-85644800	Weak transcription	NHDF-Ad	bronchial
22	chr9:85643400-85645000	Weak transcription	Esophagus	oesophagus
23	chr9:85643400-85645600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr9:85643600-85643800	Enhancers	Rectal Mucosa Donor 29	rectum

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