Variant report

Variant	rs648869
Chromosome Location	chr1:75714424-75714425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10493564	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10493565	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10493566	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10518500	0.87[CEU][hapmap];0.87[TSI][hapmap]
rs10782715	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162847	0.84[ASN][1000 genomes]
rs11162849	0.84[ASN][1000 genomes]
rs11162856	0.84[ASN][1000 genomes]
rs11162861	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162870	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162872	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162873	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162878	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162880	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11162888	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11806471	0.81[CEU][hapmap]
rs11809429	0.81[CEU][hapmap]
rs12057533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061094	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12095168	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1249796	0.81[CEU][hapmap]
rs1249797	0.81[CEU][hapmap]
rs1249807	0.81[CEU][hapmap]
rs12562352	0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12568950	0.84[ASN][1000 genomes]
rs12568990	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1335735	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1415461	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1443846	0.81[CEU][hapmap]
rs1505260	0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1505261	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1505262	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1505263	0.84[ASN][1000 genomes]
rs17096462	0.84[ASN][1000 genomes]
rs17096508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096860	0.81[CEU][hapmap]
rs17096877	0.81[CEU][hapmap]
rs17584530	0.81[CEU][hapmap]
rs1778454	0.81[CEU][hapmap]
rs1856128	1.00[JPT][hapmap]
rs2221459	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34755141	0.84[ASN][1000 genomes]
rs3845363	0.81[CEU][hapmap]
rs4369182	0.84[ASN][1000 genomes]
rs5006253	0.84[ASN][1000 genomes]
rs57612788	0.84[ASN][1000 genomes]
rs587346	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs587787	0.84[ASN][1000 genomes]
rs588098	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs588628	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588830	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs590301	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]
rs596098	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs596515	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs596620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598609	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs598649	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs60198223	0.84[ASN][1000 genomes]
rs604745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs611309	0.84[ASN][1000 genomes]
rs616827	0.84[CHD][hapmap];1.00[JPT][hapmap]
rs617196	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs619193	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs625357	1.00[CEU][hapmap]
rs629226	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632068	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs635184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs636855	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs637660	0.84[ASN][1000 genomes]
rs638302	0.84[ASN][1000 genomes]
rs639028	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs642923	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs646879	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs647924	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs648363	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs649352	0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs663620	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs664268	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs664593	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][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];1.00[ASN][1000 genomes]
rs665575	0.84[ASN][1000 genomes]
rs666397	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs667887	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs669806	0.84[ASN][1000 genomes]
rs671533	0.94[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671919	0.94[CEU][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs675962	1.00[CEU][hapmap]
rs679018	1.00[JPT][hapmap]
rs681689	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs681866	1.00[JPT][hapmap]
rs694025	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7540751	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7544408	1.00[JPT][hapmap]
rs7555803	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556057	1.00[JPT][hapmap]
rs976048	0.84[ASN][1000 genomes]

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	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997508	chr1:75709664-75748920	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs648869	SLC44A5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75701200-75715800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:75710600-75714600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:75711800-75718800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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