Variant report

Variant	rs9399023
Chromosome Location	chr6:132731358-132731359
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1000848	0.99[ASN][1000 genomes]
rs1000849	0.98[ASN][1000 genomes]
rs12660839	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12663764	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1338934	0.84[ASN][1000 genomes]
rs1338936	0.84[ASN][1000 genomes]
rs1338937	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1338938	0.98[ASN][1000 genomes]
rs1538307	0.98[ASN][1000 genomes]
rs2153175	0.98[ASN][1000 genomes]
rs2185185	0.98[ASN][1000 genomes]
rs2211095	0.94[ASN][1000 genomes]
rs2327242	0.98[ASN][1000 genomes]
rs2327243	0.88[ASN][1000 genomes]
rs2327244	0.92[ASN][1000 genomes]
rs2876186	0.98[ASN][1000 genomes]
rs2876187	0.95[ASN][1000 genomes]
rs4377800	0.94[ASN][1000 genomes]
rs4489176	0.95[ASN][1000 genomes]
rs4515403	0.95[ASN][1000 genomes]
rs4529319	0.94[ASN][1000 genomes]
rs4897580	0.95[ASN][1000 genomes]
rs6569796	0.94[ASN][1000 genomes]
rs6900501	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs6906574	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs6921325	0.95[ASN][1000 genomes]
rs6922502	0.99[ASN][1000 genomes]
rs6923916	0.99[ASN][1000 genomes]
rs6929072	0.81[ASN][1000 genomes]
rs6937815	0.95[ASN][1000 genomes]
rs6938427	0.95[ASN][1000 genomes]
rs6942368	0.94[ASN][1000 genomes]
rs73776207	0.96[ASN][1000 genomes]
rs7450274	0.98[ASN][1000 genomes]
rs7743007	0.98[ASN][1000 genomes]
rs7743456	0.98[ASN][1000 genomes]
rs7750935	0.94[ASN][1000 genomes]
rs7754992	0.95[ASN][1000 genomes]
rs7757469	0.94[ASN][1000 genomes]
rs7757641	0.94[ASN][1000 genomes]
rs7759787	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7761178	0.83[ASN][1000 genomes]
rs7770281	0.99[ASN][1000 genomes]
rs7770326	0.94[ASN][1000 genomes]
rs8180540	0.94[ASN][1000 genomes]
rs9375888	0.95[ASN][1000 genomes]
rs9385605	0.98[ASN][1000 genomes]
rs9388993	0.84[ASN][1000 genomes]
rs9388994	0.99[ASN][1000 genomes]
rs9388995	0.95[ASN][1000 genomes]
rs9399027	0.94[ASN][1000 genomes]
rs9399028	0.84[ASN][1000 genomes]
rs9402405	0.98[ASN][1000 genomes]
rs9483442	0.83[ASN][1000 genomes]
rs9493308	0.84[ASN][1000 genomes]
rs9493309	0.84[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	nsv830811	chr6:132623160-132787539	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv604668	chr6:132687248-132731358	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9399023	LTF	trans	brain	seeQTL
rs9399023	CAPS	trans	brain	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132725200-132734800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:132726400-132734200	Weak transcription	Fetal Kidney	kidney
3	chr6:132726600-132733600	Weak transcription	NHDF-Ad	bronchial
4	chr6:132727200-132733800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:132727600-132732200	Weak transcription	Osteobl	bone
6	chr6:132727800-132732200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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