Variant report

Variant	rs2484204
Chromosome Location	chr10:27738002-27738003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2478251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2484203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505321	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641792	0.89[ASN][1000 genomes]
rs72810095	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9418630	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	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
3	nsv1045257	chr10:27572440-27926946	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1053952	chr10:27659365-27915029	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv2750890	chr10:27669479-27774501	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2484204	PTCHD3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27735200-27739000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr10:27735600-27738400	Weak transcription	HMEC	breast
3	chr10:27735800-27738200	Weak transcription	NHEK	skin
4	chr10:27736000-27739000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:27736400-27738800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr10:27736400-27739000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr10:27736800-27739000	Enhancers	Primary B cells from cord blood	blood
8	chr10:27737000-27739200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:27737200-27739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:27737400-27742000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr10:27738000-27738800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:27738000-27738800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr10:27738000-27738800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:27738000-27738800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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