Variant report

Variant	rs10046046
Chromosome Location	chr5:40868580-40868581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:40833133..40835990-chr5:40867095..40868657,2	K562	blood:
2	chr5:40858083..40859601-chr5:40868438..40871076,2	K562	blood:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10035225	0.84[JPT][hapmap]
rs10035235	0.86[ASW][hapmap]
rs10035592	0.83[ASN][1000 genomes]
rs10035621	0.90[ASN][1000 genomes]
rs10041257	0.90[ASN][1000 genomes]
rs10041319	0.99[ASN][1000 genomes]
rs10054948	0.84[JPT][hapmap]
rs10058274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10060965	0.83[ASN][1000 genomes]
rs10063892	0.90[ASN][1000 genomes]
rs10072099	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10072214	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10076486	0.81[ASN][1000 genomes]
rs10077786	0.84[JPT][hapmap]
rs10080165	0.84[JPT][hapmap]
rs10472340	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10472342	0.84[JPT][hapmap]
rs10473227	0.83[ASN][1000 genomes]
rs10473228	0.83[ASN][1000 genomes]
rs10512750	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10941526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs10941527	0.84[ASN][1000 genomes]
rs1120308	0.83[ASN][1000 genomes]
rs11739731	0.83[ASN][1000 genomes]
rs11741315	0.83[ASN][1000 genomes]
rs11746650	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12109051	0.81[ASN][1000 genomes]
rs12523329	0.86[ASW][hapmap]
rs12652909	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12657195	0.83[ASN][1000 genomes]
rs12658133	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13353861	0.98[ASN][1000 genomes]
rs13353862	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13353865	0.99[ASN][1000 genomes]
rs13354307	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13355045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1393155	0.82[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs1615402	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1645519	0.81[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs16870407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16870425	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]
rs16870434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870491	0.83[ASN][1000 genomes]
rs188932	0.81[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2081153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs225749	0.88[ASN][1000 genomes]
rs2291782	0.86[ASW][hapmap]
rs2329430	0.83[ASN][1000 genomes]
rs2329431	0.90[AFR][1000 genomes]
rs2455307	0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2455308	0.92[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs28718806	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2876848	0.83[ASN][1000 genomes]
rs28770573	0.83[ASN][1000 genomes]
rs28831497	0.81[ASN][1000 genomes]
rs28834109	0.82[ASN][1000 genomes]
rs28860325	0.83[ASN][1000 genomes]
rs28870511	0.83[ASN][1000 genomes]
rs323555	0.88[ASN][1000 genomes]
rs323557	0.87[ASN][1000 genomes]
rs323558	0.86[ASN][1000 genomes]
rs323559	0.88[ASN][1000 genomes]
rs323563	0.83[ASN][1000 genomes]
rs323564	0.81[ASN][1000 genomes]
rs323566	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs34888872	0.83[ASN][1000 genomes]
rs369331	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs3792640	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3792641	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3792642	0.84[JPT][hapmap]
rs3805490	0.86[ASW][hapmap]
rs3805492	0.86[ASW][hapmap]
rs4277953	0.81[ASN][1000 genomes]
rs4277954	0.83[ASN][1000 genomes]
rs439322	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4461680	0.83[ASN][1000 genomes]
rs446920	0.88[ASN][1000 genomes]
rs4559041	0.83[ASN][1000 genomes]
rs619491	0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs62357601	0.92[ASN][1000 genomes]
rs62357603	0.92[ASN][1000 genomes]
rs62357605	0.94[ASN][1000 genomes]
rs62357612	0.99[ASN][1000 genomes]
rs62357636	0.90[ASN][1000 genomes]
rs62357641	0.90[ASN][1000 genomes]
rs62358575	0.83[ASN][1000 genomes]
rs72748000	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72749504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72749508	0.99[ASN][1000 genomes]
rs72749510	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72749514	0.90[ASN][1000 genomes]
rs72749526	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701643	0.83[ASN][1000 genomes]
rs7701871	0.83[ASN][1000 genomes]
rs7704691	0.83[ASN][1000 genomes]
rs7706776	0.83[ASN][1000 genomes]
rs7717388	0.84[JPT][hapmap]
rs7717391	0.84[JPT][hapmap]
rs7717457	0.84[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap]
rs7717794	0.83[ASN][1000 genomes]
rs7724262	0.83[ASN][1000 genomes]
rs837387	0.86[ASN][1000 genomes]
rs9292788	0.82[JPT][hapmap]
rs9292793	0.83[ASN][1000 genomes]
rs9292794	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9292795	0.83[ASN][1000 genomes]
rs972007	0.83[ASN][1000 genomes]
rs972008	0.83[ASN][1000 genomes]
rs9885543	0.83[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
rs10046046	MGC42105	cis	parietal	SCAN

Chromatin state (count:3 , 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	chr5:40867600-40871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40868000-40868600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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