Variant report

Variant	rs6876739
Chromosome Location	chr5:40938342-40938343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1063499	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1376178	0.85[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1376180	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1376181	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1450656	0.85[EUR][1000 genomes]
rs1450657	0.85[EUR][1000 genomes]
rs1697938	0.86[JPT][hapmap]
rs1901165	0.85[EUR][1000 genomes]
rs1901166	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122569	0.85[ASW][hapmap];0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2250856	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2443035	0.96[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2443040	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2455301	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2455302	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455309	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2455311	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455312	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2455314	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2459463	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2459464	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2459465	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2459467	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2597738	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2597739	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2597746	0.96[CEU][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes]
rs323565	0.82[JPT][hapmap]
rs324063	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs324066	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs324067	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs324068	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs324072	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35642126	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs364443	0.91[JPT][hapmap]
rs438652	0.91[JPT][hapmap]
rs6895963	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv880796	chr5:40934832-40985604	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6876739	OXCT1	cis	cerebellum	SCAN
rs6876739	DAB2	cis	cerebellum	SCAN
rs6876739	C5orf34	cis	parietal	SCAN
rs6876739	MGC42105	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40931200-40992200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr5:40931800-40991000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:40932800-40942000	Strong transcription	Fetal Lung	lung
4	chr5:40933400-40956400	Weak transcription	Fetal Brain Male	brain
5	chr5:40937000-40938800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:40937000-40959600	Weak transcription	Left Ventricle	heart
7	chr5:40937800-40938600	Weak transcription	Ovary	ovary

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