Variant report

Variant	rs644583
Chromosome Location	chr6:145472281-145472282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs487499	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519653	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539334	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs544611	0.83[ASN][1000 genomes]
rs548329	0.82[ASN][1000 genomes]
rs560458	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582935	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597662	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604961	0.82[ASN][1000 genomes]
rs605718	0.83[ASN][1000 genomes]
rs617778	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs624566	0.85[ASN][1000 genomes]
rs666422	0.83[ASN][1000 genomes]
rs682657	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9497196	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1022965	chr6:145374851-145635385	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv830834	chr6:145392073-145556294	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv886743	chr6:145433861-145528057	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv886744	chr6:145452401-145528057	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs644583	PLAGL1	cis	cerebellum	SCAN
rs644583	STX11	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145469800-145475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr6:145470000-145472800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:145470200-145472800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:145470400-145476800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:145471000-145473200	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:145471600-145472600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:145471600-145474600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:145472200-145472400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:145472200-145473200	Enhancers	Hela-S3	cervix

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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