Variant report

Variant	rs13100169
Chromosome Location	chr3:155154725-155154726
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11706749	0.95[ASN][1000 genomes]
rs11709568	0.95[CHD][hapmap]
rs11713552	0.81[ASN][1000 genomes]
rs11715278	1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11928089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12107115	0.84[CHD][hapmap]
rs12487150	0.83[ASN][1000 genomes]
rs12493778	0.88[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs12631218	0.82[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12634171	0.82[ASN][1000 genomes]
rs12696031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13066178	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13081656	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13083852	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs13094738	0.81[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2351	0.82[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2352	0.82[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs4524323	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4630984	0.81[CHB][hapmap]
rs4679744	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679745	0.82[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs4679746	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4679747	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4680173	0.82[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs4680174	0.86[CHD][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs4680175	0.86[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4680176	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs4680177	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs4680178	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680180	0.82[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs4680181	0.82[ASN][1000 genomes]
rs4680185	0.93[CHD][hapmap]
rs56103965	0.82[ASN][1000 genomes]
rs6440985	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs6440990	0.82[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs6440993	0.95[CHD][hapmap]
rs6440994	0.88[CHD][hapmap]
rs6440995	0.88[CHD][hapmap]
rs6802079	0.82[CHB][hapmap];1.00[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs6804318	0.82[CHB][hapmap]
rs6807784	0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs6807961	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7615026	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618495	0.95[CHD][hapmap]
rs7619730	0.82[JPT][hapmap]
rs7627097	0.82[ASN][1000 genomes]
rs9289955	0.81[ASN][1000 genomes]
rs9823946	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9829532	0.95[CHD][hapmap]
rs9841365	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs9848852	0.93[CHD][hapmap]
rs9869956	0.98[CHD][hapmap];0.80[JPT][hapmap];0.81[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	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv877679	chr3:155128968-155204939	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13100169	PLCH1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155152800-155155400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:155153200-155155800	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:155153400-155155600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:155153400-155155600	Enhancers	Osteobl	bone
5	chr3:155153800-155155600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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