Variant report

Variant	rs2020155
Chromosome Location	chr10:27740194-27740195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10508725	0.81[ASN][1000 genomes]
rs11015783	1.00[ASN][1000 genomes]
rs11814298	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11814433	0.91[ASN][1000 genomes]
rs12413104	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414736	1.00[ASN][1000 genomes]
rs12415979	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs12772577	0.91[ASN][1000 genomes]
rs12777582	0.91[ASN][1000 genomes]
rs17681969	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17749271	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17749397	0.91[ASN][1000 genomes]
rs2368231	0.91[ASN][1000 genomes]
rs2642274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2992007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34354872	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34467586	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34773871	1.00[ASN][1000 genomes]
rs34978206	0.91[ASN][1000 genomes]
rs35224308	0.91[ASN][1000 genomes]
rs35590474	0.91[ASN][1000 genomes]
rs35599449	0.91[ASN][1000 genomes]
rs35673366	1.00[ASN][1000 genomes]
rs3847381	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3904627	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4749249	0.91[ASN][1000 genomes]
rs56108042	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs594549	0.91[ASN][1000 genomes]
rs616550	0.83[ASN][1000 genomes]
rs620664	0.83[ASN][1000 genomes]
rs625433	0.91[ASN][1000 genomes]
rs638324	0.83[ASN][1000 genomes]
rs661882	0.91[ASN][1000 genomes]
rs67199203	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68016309	1.00[ASN][1000 genomes]
rs7067807	1.00[ASN][1000 genomes]
rs7069133	1.00[ASN][1000 genomes]
rs7090220	0.91[ASN][1000 genomes]
rs7095624	1.00[ASN][1000 genomes]
rs717287	0.91[ASN][1000 genomes]
rs765700	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9732977	0.91[ASN][1000 genomes]
rs9804355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[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
rs2020155	PTCHD3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27737400-27742000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr10:27738800-27741600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr10:27739000-27740400	Weak transcription	Primary B cells from cord blood	blood
4	chr10:27739000-27741600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:27739600-27746600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:27740000-27750000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links