Variant report

Variant	rs2547455
Chromosome Location	chr5:75346102-75346103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13162056	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13174796	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393205	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1423103	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1423104	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1501905	0.82[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.80[YRI][hapmap]
rs1553310	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs183766	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs183767	0.87[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs187285	0.87[CEU][hapmap];0.80[CHB][hapmap];0.87[JPT][hapmap]
rs1910051	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2254153	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs258612	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs258613	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs258614	0.81[CEU][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs258621	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[YRI][hapmap]
rs2731732	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731733	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731735	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28620	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28621	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2937705	0.87[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap]
rs30191	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30192	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30196	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30197	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs30198	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30199	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs30202	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs30204	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30205	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30206	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs30249	0.87[JPT][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes]
rs7378518	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7443455	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7443586	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs993914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2547455	OR2G3	trans	cerebellum	SCAN
rs2547455	CTC-235G5.3	cis	Nerve Tibial	GTEx
rs2547455	ARSB	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75345400-75346600	Enhancers	HMEC	breast
2	chr5:75345600-75346200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:75345600-75346400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:75345800-75346200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:75345800-75346400	Enhancers	NHEK	skin

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