Variant report

Variant	rs1754054
Chromosome Location	chr9:93131408-93131409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10761349	0.88[ASN][1000 genomes]
rs10821371	0.90[ASN][1000 genomes]
rs10993252	0.86[ASN][1000 genomes]
rs10993310	0.81[ASN][1000 genomes]
rs1329090	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1343100	0.92[ASN][1000 genomes]
rs1343101	0.89[ASN][1000 genomes]
rs1571452	0.90[ASN][1000 genomes]
rs1627667	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630044	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1648473	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1648475	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648476	0.93[ASN][1000 genomes]
rs1754055	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1754056	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1754059	0.92[ASN][1000 genomes]
rs1776994	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1776995	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1777013	0.92[ASN][1000 genomes]
rs1777025	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1889205	0.90[ASN][1000 genomes]
rs1983962	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2004205	0.88[ASN][1000 genomes]
rs2386534	0.82[ASN][1000 genomes]
rs2555061	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555065	0.94[ASN][1000 genomes]
rs2555066	0.94[ASN][1000 genomes]
rs2555067	0.93[ASN][1000 genomes]
rs2555068	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2771077	0.94[ASN][1000 genomes]
rs2798043	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798049	0.94[ASN][1000 genomes]
rs2798050	0.92[ASN][1000 genomes]
rs2798053	0.90[ASN][1000 genomes]
rs752788	0.88[ASN][1000 genomes]
rs7862861	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051180	chr9:92869383-93141038	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv540169	chr9:92869383-93141038	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1041278	chr9:92965701-93560454	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv528155	chr9:93106543-93152717	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv516680	chr9:93116944-93138600	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv482748	chr9:93123377-93279526	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv893565	chr9:93130796-93392332	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1754054	RP11-389K14.3	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93130200-93132200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr9:93130600-93132200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr9:93130600-93132400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:93131200-93131600	Enhancers	H1 Cell Line	embryonic stem cell
5	chr9:93131200-93131600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:93131200-93131800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:93131200-93132200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr9:93131200-93132400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr9:93131400-93131800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:93131400-93131800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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