Variant report

Variant	rs12185387
Chromosome Location	chr18:8001853-8001854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11081349	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11081353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11660124	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11660294	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11661715	0.87[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs11664885	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11873208	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873445	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876715	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12956144	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13381562	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1468707	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17396187	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17476082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1942957	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2044220	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs4461180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8088882	0.87[CEU][hapmap];0.82[CHB][hapmap]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12185387	PTPRM	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7987600-8033400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:7988200-8003600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:7999400-8002000	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr18:7999600-8004200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr18:8000000-8004000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr18:8000200-8003600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr18:8000200-8004200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:8000800-8002200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:8001000-8007600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr18:8001400-8002600	Weak transcription	Aorta	Aorta
11	chr18:8001400-8004000	Weak transcription	Left Ventricle	heart
12	chr18:8001400-8004200	Weak transcription	Right Ventricle	heart
13	chr18:8001400-8005600	Weak transcription	Psoas Muscle	Psoas
14	chr18:8001400-8006600	Weak transcription	Lung	lung
15	chr18:8001400-8029200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:8001400-8029200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:8001600-8003800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr18:8001600-8004000	Weak transcription	Right Atrium	heart
19	chr18:8001800-8002000	Enhancers	Fetal Heart	heart
20	chr18:8001800-8002800	Strong transcription	A549	lung

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