Variant report

Variant	rs9952873
Chromosome Location	chr18:8044421-8044422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr18:8044365-8044469	MCF10A-Er-Src	breast:	n/a	chr18:8044427-8044434 chr18:8044427-8044435
2	STAT3	chr18:8044309-8044579	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
PTPRM	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12103962	0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2099932	0.82[ASW][hapmap];0.83[AMR][1000 genomes]
rs28367342	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28379285	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28478486	0.82[AFR][1000 genomes]
rs28511885	0.88[AFR][1000 genomes]
rs28521877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28526245	1.00[AFR][1000 genomes]
rs28557220	1.00[ASW][hapmap];0.94[AFR][1000 genomes]
rs28569201	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28611270	0.94[AFR][1000 genomes]
rs28709298	1.00[AFR][1000 genomes]
rs73385648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73385649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73385658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73385659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9948263	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9949297	0.83[AMR][1000 genomes]
rs9950590	1.00[ASW][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9951610	0.91[AFR][1000 genomes]
rs9952921	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9953560	0.82[AFR][1000 genomes]
rs9955097	1.00[ASW][hapmap];0.83[AMR][1000 genomes]
rs9955973	0.83[AMR][1000 genomes]
rs9958058	0.83[AMR][1000 genomes]
rs9963151	0.88[AFR][1000 genomes]
rs9963467	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9965217	0.82[AFR][1000 genomes]
rs9966934	0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv909359	chr18:8001853-8064021	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:8021200-8052000	Weak transcription	Psoas Muscle	Psoas
2	chr18:8030000-8056400	Weak transcription	Pancreas	Pancrea
3	chr18:8037000-8045400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr18:8038600-8045000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:8041400-8048200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr18:8041800-8047600	Weak transcription	A549	lung
7	chr18:8042000-8048800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr18:8042600-8044600	Enhancers	Left Ventricle	heart
9	chr18:8042800-8050200	Weak transcription	Gastric	stomach
10	chr18:8043000-8048000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:8043000-8049800	Weak transcription	Lung	lung
12	chr18:8043200-8045600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr18:8043200-8052000	Weak transcription	Right Atrium	heart
14	chr18:8043400-8050800	Weak transcription	Right Ventricle	heart
15	chr18:8043400-8052000	Weak transcription	Ovary	ovary
16	chr18:8044400-8044600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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