Variant report

Variant	rs16870425
Chromosome Location	chr5:40865863-40865864
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40861136..40863091-chr5:40865638..40868114,2	K562	blood:
2	chr5:40840448..40842077-chr5:40865618..40867918,2	K562	blood:
3	chr5:40833348..40835885-chr5:40864377..40867574,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction
ENSG00000132357	Chromatin interaction

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10035225	0.95[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs10035592	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10035621	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10041257	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10041319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10046046	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.99[ASN][1000 genomes]
rs10051758	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10051888	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10054615	0.97[EUR][1000 genomes]
rs10054948	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10056047	0.86[EUR][1000 genomes]
rs10056708	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10058274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10059679	0.94[EUR][1000 genomes]
rs10060965	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10063892	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10066847	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10072099	0.90[ASN][1000 genomes]
rs10072128	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10072214	0.82[ASN][1000 genomes]
rs10073246	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10076486	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10076663	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10077786	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10078706	0.97[EUR][1000 genomes]
rs10079875	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10080165	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10472340	0.90[ASN][1000 genomes]
rs10472342	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[EUR][1000 genomes]
rs10472344	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10473219	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10473220	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10473221	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10473227	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10473228	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10512750	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10941526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10941527	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1120308	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11739731	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11741315	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11746650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11748194	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12109051	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652909	0.90[ASN][1000 genomes]
rs12657195	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12658133	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12659571	0.90[EUR][1000 genomes]
rs13353861	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13353862	0.98[ASN][1000 genomes]
rs13353865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13354307	0.99[ASN][1000 genomes]
rs13354561	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13355045	0.99[ASN][1000 genomes]
rs13360188	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1393155	1.00[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1393156	0.90[EUR][1000 genomes]
rs1615402	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1645519	1.00[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs16870434	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.99[ASN][1000 genomes]
rs16870491	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1697939	0.93[EUR][1000 genomes]
rs1697940	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1697941	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1697942	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1827363	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1827366	0.96[EUR][1000 genomes]
rs1827367	0.94[EUR][1000 genomes]
rs188932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2081153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225749	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329430	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2432155	0.91[EUR][1000 genomes]
rs2455303	0.86[EUR][1000 genomes]
rs2455307	0.95[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2455308	0.95[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28718806	0.85[ASN][1000 genomes]
rs2876848	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28770573	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28831497	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28834109	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28860325	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28870511	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs323555	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323557	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs323558	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs323559	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs323563	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs323564	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs323566	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34888872	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs369331	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[LWK][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs373411	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3792640	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3792641	0.95[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3792642	0.84[CEU][hapmap];0.84[JPT][hapmap]
rs4277953	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4277954	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs439322	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4461680	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs446920	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4559041	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs567165	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs619491	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62357063	0.86[EUR][1000 genomes]
rs62357601	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357603	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62357605	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62357612	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357636	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62357641	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62358575	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62358580	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs72748000	0.92[ASN][1000 genomes]
rs72749504	0.99[ASN][1000 genomes]
rs72749508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749510	0.90[ASN][1000 genomes]
rs72749514	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72749521	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72749526	0.83[ASN][1000 genomes]
rs7445411	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7701643	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701662	0.87[EUR][1000 genomes]
rs7701871	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7704691	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7706776	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7711745	0.93[EUR][1000 genomes]
rs7716062	0.86[EUR][1000 genomes]
rs7717388	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7717391	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7717457	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7717794	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7721703	0.87[EUR][1000 genomes]
rs7724262	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7731772	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7731944	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7733440	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs837387	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9292788	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs9292790	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9292793	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9292794	0.83[ASN][1000 genomes]
rs9292795	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9292798	0.86[EUR][1000 genomes]
rs972007	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs972008	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9885543	0.87[EUR][1000 genomes];0.84[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	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	esv3444044	chr5:40860244-40888483	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16870425	OXCT1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40856200-40871400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:40865000-40866600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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