Variant report

Variant	rs564474
Chromosome Location	chr19:39482866-39482867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39463902..39468166-chr19:39481620..39485046,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10409280	0.81[JPT][hapmap]
rs12609745	0.82[ASN][1000 genomes]
rs12610086	0.81[ASN][1000 genomes]
rs13313727	0.82[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1627631	0.80[CHB][hapmap]
rs1654334	0.81[AFR][1000 genomes]
rs1654335	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654337	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1672656	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672657	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1672658	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1672659	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17795157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473604	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs482342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs483359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498586	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs500660	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs500691	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs555858	0.93[ASN][1000 genomes]
rs55829324	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56111444	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs563627	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs572764	0.80[CHB][hapmap]
rs57588219	0.80[ASN][1000 genomes]
rs581978	0.86[YRI][hapmap]
rs586159	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs606372	0.80[AFR][1000 genomes]
rs62121526	0.87[ASN][1000 genomes]
rs622528	0.80[AFR][1000 genomes]
rs637972	0.88[AFR][1000 genomes]
rs650027	0.92[AFR][1000 genomes]
rs662202	0.80[CHB][hapmap]
rs667911	0.82[ASN][1000 genomes]
rs678772	0.80[CHB][hapmap]
rs678885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248728	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7249730	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72623865	0.83[ASN][1000 genomes]
rs7508413	0.81[AFR][1000 genomes]
rs930100	0.80[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs564474	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs564474	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs564474	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs564474	FBXO27	cis	Esophagus Mucosa	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39479000-39483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:39480000-39483800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:39480000-39503400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:39480200-39483800	Weak transcription	HSMMtube	muscle
5	chr19:39480200-39486600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:39481000-39516000	Weak transcription	Brain Angular Gyrus	brain
7	chr19:39481600-39484400	Enhancers	HMEC	breast
8	chr19:39481800-39484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:39482200-39483000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:39482200-39483200	Weak transcription	HUVEC	blood vessel
11	chr19:39482200-39483600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:39482200-39483600	Weak transcription	A549	lung
13	chr19:39482200-39483600	Weak transcription	Hela-S3	cervix
14	chr19:39482200-39483600	Weak transcription	NHDF-Ad	bronchial
15	chr19:39482200-39483800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:39482400-39483400	Weak transcription	Osteobl	bone
17	chr19:39482400-39483800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:39482400-39483800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:39482400-39484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:39482600-39483000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:39482600-39483800	Weak transcription	Muscle Satellite Cultured Cells	--

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