Variant report

Variant	rs3116602
Chromosome Location	chr13:51111355-51111356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1262775	0.82[TSI][hapmap]
rs1262870	1.00[AFR][1000 genomes]
rs1327646	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1341637	0.91[EUR][1000 genomes]
rs157165	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1630605	0.82[TSI][hapmap]
rs1638703	0.84[TSI][hapmap]
rs201754	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs201755	0.83[ASN][1000 genomes]
rs201757	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs201762	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2225226	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408045	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3116598	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3116599	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116600	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116607	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116613	0.92[EUR][1000 genomes]
rs3116615	0.92[EUR][1000 genomes]
rs3116616	0.91[EUR][1000 genomes]
rs3116617	0.92[EUR][1000 genomes]
rs3118903	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3118905	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118906	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118909	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118910	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118915	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118918	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118919	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3118920	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3121212	1.00[ASW][hapmap]
rs495838	0.82[TSI][hapmap]
rs7337757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391952	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3116602	LPAR6	cis	parietal	SCAN
rs3116602	ATP7B	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51110000-51113600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:51110200-51111400	Enhancers	HUVEC	blood vessel
3	chr13:51110400-51111400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr13:51110400-51111400	Enhancers	NH-A	brain
5	chr13:51110400-51111400	Enhancers	NHDF-Ad	bronchial
6	chr13:51110400-51111600	Enhancers	HMEC	breast
7	chr13:51110600-51111400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr13:51110600-51111400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:51110600-51111400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr13:51110600-51111400	Enhancers	NHEK	skin
11	chr13:51110800-51111400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:51111000-51111400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:51111200-51111400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:51111200-51113600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:51111200-51113600	Weak transcription	Osteobl	bone

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