Variant report

Variant	rs1423246
Chromosome Location	chr5:59661456-59661457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10461451	0.89[JPT][hapmap]
rs1115372	0.91[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12054887	0.84[JPT][hapmap]
rs12653863	0.89[JPT][hapmap]
rs13165296	0.81[GIH][hapmap]
rs13166747	0.88[JPT][hapmap]
rs13171028	0.89[JPT][hapmap]
rs13172481	0.81[GIH][hapmap]
rs1363862	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1423247	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs16874969	0.81[GIH][hapmap]
rs17839379	0.88[ASW][hapmap];0.81[LWK][hapmap]
rs2910629	0.82[ASW][hapmap]
rs4349679	0.83[GIH][hapmap];0.84[JPT][hapmap]
rs4394088	0.85[GIH][hapmap];0.84[JPT][hapmap]
rs4409049	0.90[JPT][hapmap]
rs4580739	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699955	0.82[ASN][1000 genomes]
rs6449467	0.89[JPT][hapmap]
rs6860887	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6862735	0.81[GIH][hapmap]
rs6878055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897671	0.93[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7711093	0.81[GIH][hapmap]
rs7714394	0.96[CEU][hapmap];0.84[JPT][hapmap]
rs7733705	0.81[GIH][hapmap]
rs7737905	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918592	0.82[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59647200-59694200	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59649400-59668200	Weak transcription	Gastric	stomach
3	chr5:59650400-59674800	Weak transcription	Aorta	Aorta
4	chr5:59658000-59663600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:59658200-59665600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:59658400-59662000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:59660000-59666800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:59661200-59661600	Enhancers	Placenta	Placenta
9	chr5:59661400-59661600	Enhancers	Stomach Mucosa	stomach
10	chr5:59661400-59668000	Weak transcription	HepG2	liver

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