Variant report

Variant	rs1329090
Chromosome Location	chr9:93109390-93109391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10761349	0.83[ASN][1000 genomes]
rs10821371	0.84[ASN][1000 genomes]
rs10993252	0.81[ASN][1000 genomes]
rs1343100	0.87[ASN][1000 genomes]
rs1343101	0.84[ASN][1000 genomes]
rs1571452	0.85[ASN][1000 genomes]
rs1627667	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1630044	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648473	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648475	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1648476	0.88[ASN][1000 genomes]
rs1754054	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1754055	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1754056	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1754059	0.87[ASN][1000 genomes]
rs1776994	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1776995	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1777013	0.87[ASN][1000 genomes]
rs1777025	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889205	0.84[ASN][1000 genomes]
rs1983962	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2004205	0.83[ASN][1000 genomes]
rs2555061	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555065	0.89[ASN][1000 genomes]
rs2555066	0.89[ASN][1000 genomes]
rs2555067	0.88[ASN][1000 genomes]
rs2555068	0.87[ASN][1000 genomes]
rs2771077	0.89[ASN][1000 genomes]
rs2798043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2798049	0.88[ASN][1000 genomes]
rs2798050	0.87[ASN][1000 genomes]
rs2798053	0.85[ASN][1000 genomes]
rs752788	0.83[ASN][1000 genomes]
rs7862861	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv893564	chr9:93074228-93116944	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1329090	RP11-389K14.3	cis	lung	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93103000-93111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:93106400-93111800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:93106600-93109600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:93106600-93109600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:93106600-93110000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:93108200-93109600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:93108400-93109800	Weak transcription	NHEK	skin

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