Variant report

Variant	rs542538
Chromosome Location	chr6:49298050-49298051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs476180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs479383	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs492172	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs493184	0.82[AMR][1000 genomes]
rs493700	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525559	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs528451	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539581	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs540785	0.81[AFR][1000 genomes]
rs555933	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562077	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap]
rs579846	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs542538	CENPQ	cis	lung	GTEx
rs542538	CENPQ	cis	Artery Tibial	GTEx
rs542538	CENPQ	cis	Nerve Tibial	GTEx
rs542538	DEFB114	cis	cerebellum	SCAN
rs542538	CENPQ	cis	Adipose Subcutaneous	GTEx
rs542538	CENPQ	cis	lymphoblastoid	seeQTL
rs542538	TDRD6	cis	cerebellum	SCAN
rs542538	CENPQ	cis	Esophagus Muscularis	GTEx
rs542538	CENPQ	cis	Esophagus Mucosa	GTEx
rs542538	CENPQ	cis	Thyroid	GTEx
rs542538	MUT	cis	Nerve Tibial	GTEx
rs542538	C6orf139	cis	multi-tissue	Pritchard
rs542538	CENPQ	cis	Muscle Skeletal	GTEx
rs542538	CENPQ	cis	multi-tissue	Pritchard
rs542538	MUT	cis	multi-tissue	Pritchard
rs542538	CENPQ	cis	Artery Aorta	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49295000-49310200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:49295400-49300800	Weak transcription	HMEC	breast
3	chr6:49295400-49304200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:49295400-49309400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:49296000-49304400	Weak transcription	Aorta	Aorta
6	chr6:49296200-49300000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:49296200-49302600	Weak transcription	HUVEC	blood vessel
8	chr6:49296400-49300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:49297800-49298200	Enhancers	Fetal Lung	lung
10	chr6:49297800-49298400	Enhancers	Rectal Smooth Muscle	rectum

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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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