Variant report

Variant	rs3116607
Chromosome Location	chr13:51122118-51122119
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1327646	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1341637	0.81[EUR][1000 genomes]
rs157165	0.83[ASN][1000 genomes]
rs201754	0.83[ASN][1000 genomes]
rs201755	0.83[ASN][1000 genomes]
rs201757	0.83[ASN][1000 genomes]
rs201762	1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs2225226	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408045	0.83[EUR][1000 genomes]
rs3116599	1.00[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3116600	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116601	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116602	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116603	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116604	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116605	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116606	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116613	0.83[EUR][1000 genomes]
rs3116615	0.83[EUR][1000 genomes]
rs3116616	0.82[EUR][1000 genomes]
rs3116617	0.83[EUR][1000 genomes]
rs3118903	0.91[ASN][1000 genomes]
rs3118905	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118906	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3118909	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118910	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118912	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118913	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118914	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118915	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118918	0.83[EUR][1000 genomes]
rs3118919	0.81[EUR][1000 genomes]
rs3118920	0.83[EUR][1000 genomes]
rs3121212	1.00[ASW][hapmap]
rs7337757	0.88[AMR][1000 genomes];0.87[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3116607	LPAR6	cis	parietal	SCAN
rs3116607	ATP7B	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51117600-51122400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr13:51118000-51122600	Weak transcription	Adipose Nuclei	Adipose
3	chr13:51118000-51123000	Weak transcription	Fetal Muscle Leg	muscle
4	chr13:51118400-51122200	Weak transcription	Fetal Heart	heart
5	chr13:51120000-51123000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr13:51120000-51126400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:51122000-51123000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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