Variant report

Variant	rs2044220
Chromosome Location	chr18:7964648-7964649
allele	C/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]
rs11081348	0.82[CHB][hapmap]
rs11081349	0.87[CEU][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap]
rs11081353	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs11660124	0.87[CEU][hapmap]
rs11661715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12185387	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]
rs12456263	0.84[EUR][1000 genomes]
rs12456376	0.82[CHB][hapmap]
rs12956144	1.00[CEU][hapmap]
rs13381562	0.82[CHB][hapmap]
rs1443618	0.82[CHB][hapmap]
rs1468707	0.87[CEU][hapmap];0.89[MEX][hapmap]
rs1561999	0.82[CHB][hapmap]
rs17396187	1.00[CEU][hapmap]
rs17476082	1.00[ASW][hapmap];0.87[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.90[AFR][1000 genomes]
rs4461180	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs6506543	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs8088882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8093794	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][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	nsv521059	chr18:7962217-7981018	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2044220	PTPRM	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7941800-7966400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr18:7947200-7981400	Weak transcription	Fetal Stomach	stomach
3	chr18:7947400-7965600	Weak transcription	Thymus	Thymus
4	chr18:7947800-7967600	Weak transcription	Primary T cells from cord blood	blood
5	chr18:7948000-7965800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr18:7948000-7967200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr18:7948000-7975000	Weak transcription	Pancreas	Pancrea
8	chr18:7951600-7965800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:7954400-7966000	Weak transcription	Fetal Kidney	kidney
10	chr18:7955400-7965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:7956000-7965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr18:7956000-7966200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr18:7956000-7980800	Weak transcription	Fetal Thymus	thymus
14	chr18:7956000-7982400	Weak transcription	Fetal Muscle Leg	muscle
15	chr18:7957600-7965200	Weak transcription	Lung	lung
16	chr18:7957600-7980600	Weak transcription	Right Ventricle	heart
17	chr18:7959000-7987400	Weak transcription	Ovary	ovary
18	chr18:7959200-7982400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr18:7959800-7965400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:7959800-7967800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr18:7960800-7967000	Weak transcription	Fetal Lung	lung
22	chr18:7961200-7964800	Enhancers	A549	lung
23	chr18:7962600-7974000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr18:7963400-7964800	Enhancers	Adipose Nuclei	Adipose
25	chr18:7963600-7965000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr18:7963800-7964800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:7963800-7965000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr18:7963800-7965400	Weak transcription	Right Atrium	heart
29	chr18:7963800-7969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr18:7963800-7977400	Weak transcription	Aorta	Aorta
31	chr18:7964000-7965200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr18:7964000-7965200	Weak transcription	Left Ventricle	heart
33	chr18:7964000-7965200	Weak transcription	Psoas Muscle	Psoas
34	chr18:7964200-7965000	Enhancers	Hela-S3	cervix
35	chr18:7964400-7964800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr18:7964400-7964800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr18:7964400-7967000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr18:7964600-7966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr18:7964600-7966800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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