Variant report

Variant	rs2815542
Chromosome Location	chr10:27950798-27950799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12354830	0.96[ASN][1000 genomes]
rs1542792	0.96[ASN][1000 genomes]
rs1628869	0.96[ASN][1000 genomes]
rs1687726	0.94[ASN][1000 genomes]
rs2007516	0.99[ASN][1000 genomes]
rs2172084	0.96[ASN][1000 genomes]
rs2637281	0.98[ASN][1000 genomes]
rs2637286	0.98[ASN][1000 genomes]
rs2637299	0.96[ASN][1000 genomes]
rs2637310	0.96[ASN][1000 genomes]
rs2637329	0.96[ASN][1000 genomes]
rs2637330	0.96[ASN][1000 genomes]
rs2642276	0.96[ASN][1000 genomes]
rs2642278	0.96[ASN][1000 genomes]
rs2642282	0.96[ASN][1000 genomes]
rs2642296	0.98[ASN][1000 genomes]
rs2642305	0.95[ASN][1000 genomes]
rs2642306	0.95[ASN][1000 genomes]
rs2642309	0.96[ASN][1000 genomes]
rs2808261	0.96[ASN][1000 genomes]
rs2808266	0.96[ASN][1000 genomes]
rs2808274	0.95[ASN][1000 genomes]
rs2808275	0.96[ASN][1000 genomes]
rs2808276	0.98[ASN][1000 genomes]
rs2808291	0.95[ASN][1000 genomes]
rs2815505	0.96[ASN][1000 genomes]
rs2815508	0.96[ASN][1000 genomes]
rs2815511	0.96[ASN][1000 genomes]
rs2815512	0.96[ASN][1000 genomes]
rs2815519	0.96[ASN][1000 genomes]
rs2815528	0.96[ASN][1000 genomes]
rs2815534	0.96[ASN][1000 genomes]
rs2815543	0.98[ASN][1000 genomes]
rs2932914	0.96[ASN][1000 genomes]
rs903282	0.95[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	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv894985	chr10:27869503-27957785	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv894986	chr10:27904646-27957785	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2815542	PTCHD3	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27933800-27963600	Weak transcription	Ovary	ovary
2	chr10:27941600-27963600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:27947000-27951000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:27947200-27951400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:27947800-27950800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr10:27948400-27950800	Weak transcription	NHDF-Ad	bronchial
7	chr10:27948600-27951000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:27948600-27954200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:27948800-27951800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:27949200-27951000	Enhancers	Adipose Nuclei	Adipose
11	chr10:27949400-27951200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr10:27949600-27951200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr10:27949800-27950800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:27950400-27950800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:27950400-27950800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr10:27950400-27950800	Flanking Active TSS	Osteobl	bone
17	chr10:27950400-27951000	Enhancers	HSMM	muscle
18	chr10:27950400-27951000	Enhancers	HSMMtube	muscle
19	chr10:27950400-27953400	Enhancers	Hela-S3	cervix
20	chr10:27950600-27950800	Enhancers	HMEC	breast
21	chr10:27950600-27951000	Enhancers	Monocytes-CD14+_RO01746	blood

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