Variant report

Variant	rs10965099
Chromosome Location	chr9:21682759-21682760
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	chr9:21681458..21682986-chr9:21704343..21706212,2	MCF-7	breast:
2	chr9:21678019..21679658-chr9:21681885..21684334,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10117244	0.86[CHD][hapmap]
rs10465050	0.80[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10811581	1.00[CEU][hapmap];0.92[JPT][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10965098	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10965101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5002625	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029634	chr9:21542970-21765286	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015623	chr9:21579110-21694039	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv892742	chr9:21589041-21707372	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892743	chr9:21675545-21772064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10965099	MTAP	cis	parietal	SCAN
rs10965099	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21677200-21684600	Enhancers	Hela-S3	cervix
2	chr9:21678000-21683200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:21678000-21688200	Enhancers	HMEC	breast
4	chr9:21678200-21684000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:21678400-21687400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:21678600-21684600	Enhancers	HUVEC	blood vessel
7	chr9:21680400-21683400	Enhancers	HSMM	muscle
8	chr9:21680400-21684200	Enhancers	NHLF	lung
9	chr9:21680400-21684600	Enhancers	NH-A	brain
10	chr9:21680400-21685000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr9:21680400-21686000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr9:21680400-21688200	Flanking Active TSS	A549	lung
13	chr9:21680400-21688200	Enhancers	Osteobl	bone
14	chr9:21680400-21691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:21681200-21682800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:21681400-21684400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:21681600-21684400	Enhancers	Stomach Mucosa	stomach
18	chr9:21682000-21683000	Weak transcription	Small Intestine	intestine
19	chr9:21682000-21683200	Enhancers	NHEK	skin
20	chr9:21682000-21683400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:21682200-21683200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr9:21682200-21683400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:21682200-21687800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr9:21682200-21688000	Enhancers	NHDF-Ad	bronchial
25	chr9:21682600-21683400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links