Variant report

Variant	rs6770862
Chromosome Location	chr3:145760929-145760930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12496198	0.89[CEU][hapmap]
rs12496358	0.84[CEU][hapmap]
rs13327094	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375578	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449438	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449439	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449440	0.82[CHB][hapmap]
rs1449444	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs1584489	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1613698	0.80[CHB][hapmap]
rs1707465	0.82[CHB][hapmap]
rs2029137	0.82[CHB][hapmap]
rs2864793	0.89[CEU][hapmap]
rs3792341	0.82[CHB][hapmap]
rs3804664	0.88[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs3804665	0.81[CHB][hapmap]
rs4681112	0.81[EUR][1000 genomes]
rs4681294	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs4681299	0.89[CEU][hapmap]
rs6710	0.82[CHB][hapmap]
rs6795690	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6799720	0.82[CHB][hapmap]
rs6801418	0.82[CHB][hapmap]
rs6802384	0.82[CHB][hapmap]
rs7614409	0.82[CHB][hapmap]
rs764755	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs7647911	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289712	0.81[EUR][1000 genomes]
rs9289713	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs9289716	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs959329	0.82[CHB][hapmap]
rs963591	0.81[EUR][1000 genomes]
rs9849076	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852153	0.84[CEU][hapmap]
rs9857975	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9862005	0.83[EUR][1000 genomes]
rs9867807	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9874627	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9877411	0.88[CEU][hapmap]

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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6770862	PLOD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145739400-145768600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:145752400-145768200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:145752600-145767600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:145752600-145775800	Weak transcription	Osteobl	bone
5	chr3:145752600-145776000	Weak transcription	HSMM	muscle
6	chr3:145760600-145761600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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