Variant report

Variant	rs4140498
Chromosome Location	chr6:49290172-49290173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1122991	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124971	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189573	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12202524	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206030	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12208066	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2143728	0.81[AFR][1000 genomes]
rs35810477	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3930746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4715127	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4715128	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544378	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9463467	0.81[AFR][1000 genomes]
rs9463469	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9473528	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9473535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755862	chr6:49081541-49298041	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3434790	chr6:49281547-49295228	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	n/a	n/a	inside rSNPs	n/a
3	esv3472555	chr6:49281568-49295231	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS	n/a	n/a	inside rSNPs	n/a
4	esv3472556	chr6:49281633-49295152	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
5	esv3472557	chr6:49281695-49295113	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
6	esv13429	chr6:49281885-49295108	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	n/a
7	esv2762590	chr6:49286305-49295370	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	n/a
8	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4140498	MUT	cis	Artery Tibial	GTEx
rs4140498	CENPQ	cis	Esophagus Muscularis	GTEx
rs4140498	MUT	cis	Nerve Tibial	GTEx
rs4140498	CENPQ	cis	Thyroid	GTEx
rs4140498	MUT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49285000-49293600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:49288400-49293800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:49289400-49290200	Enhancers	Fetal Lung	lung

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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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