Variant report

Variant	rs570475
Chromosome Location	chr6:49327918-49327919
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1738334	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1924989	0.83[JPT][hapmap]
rs3930746	0.84[JPT][hapmap]
rs476180	0.84[YRI][hapmap]
rs493700	0.86[AFR][1000 genomes]
rs504213	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs539581	0.82[YRI][hapmap]
rs540785	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556046	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs562112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs571140	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9473535	0.84[JPT][hapmap]

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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv915806	chr6:49313295-49430422	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv462943	chr6:49319025-49376924	Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv603080	chr6:49319025-49376924	Enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs570475	CENPQ	cis	Esophagus Muscularis	GTEx
rs570475	CENPQ	cis	Thyroid	GTEx
rs570475	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs570475	CENPQ	cis	Adipose Subcutaneous	GTEx
rs570475	MUT	cis	Artery Tibial	GTEx
rs570475	MUT	cis	Nerve Tibial	GTEx
rs570475	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs570475	CENPQ	cis	lung	GTEx
rs570475	CENPQ	cis	Nerve Tibial	GTEx
rs570475	CENPQ	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49310800-49328000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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