Variant report

Variant	rs10124624
Chromosome Location	chr9:15519811-15519812
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10119931	1.00[CEU][hapmap]
rs10125713	1.00[CEU][hapmap]
rs10283923	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10283927	0.81[ASN][1000 genomes]
rs1041529	1.00[CEU][hapmap]
rs10962048	0.89[JPT][hapmap]
rs12336503	0.81[ASN][1000 genomes]
rs12336509	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12339417	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12380487	0.82[CHB][hapmap]
rs12683553	0.81[ASN][1000 genomes]
rs16933311	0.89[JPT][hapmap]
rs16933348	0.83[ASN][1000 genomes]
rs1828383	0.96[ASN][1000 genomes]
rs2175257	0.81[ASN][1000 genomes]
rs2665503	1.00[CEU][hapmap]
rs2665511	1.00[CEU][hapmap]
rs2665512	1.00[CEU][hapmap]
rs2795124	1.00[CEU][hapmap]
rs2795127	1.00[CEU][hapmap]
rs2821530	1.00[CEU][hapmap]
rs56361298	0.83[ASN][1000 genomes]
rs57467578	0.83[ASN][1000 genomes]
rs58607272	0.96[ASN][1000 genomes]
rs62571010	0.81[ASN][1000 genomes]
rs62571022	0.83[ASN][1000 genomes]
rs62571023	0.83[ASN][1000 genomes]
rs62571024	0.83[ASN][1000 genomes]
rs62571027	0.88[ASN][1000 genomes]
rs62571030	0.98[ASN][1000 genomes]
rs62571031	0.96[ASN][1000 genomes]
rs62571032	0.96[ASN][1000 genomes]
rs6474927	0.98[ASN][1000 genomes]
rs7018658	0.81[ASN][1000 genomes]
rs73408328	0.83[ASN][1000 genomes]
rs73644657	0.98[ASN][1000 genomes]
rs7852774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7856318	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7856710	0.96[ASN][1000 genomes]
rs7857933	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7860339	1.00[CEU][hapmap]
rs909323	1.00[CEU][hapmap]
rs926154	1.00[CEU][hapmap]
rs9298729	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10124624	CCDC171	cis	Esophagus Mucosa	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15513400-15521800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:15513600-15521400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:15513800-15521400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:15514600-15521200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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