Variant report

Variant	rs500660
Chromosome Location	chr19:39483810-39483811
allele	C/T
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:
2	chr19:39478331..39480125-chr19:39483725..39485536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10409280	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs12609745	0.83[ASN][1000 genomes]
rs12610086	0.81[ASN][1000 genomes]
rs13313727	0.89[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654334	0.81[AFR][1000 genomes]
rs1654335	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654336	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672656	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672657	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672658	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672659	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795157	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482342	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483359	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs498586	0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs500691	0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs555858	0.94[ASN][1000 genomes]
rs55829324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56111444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563627	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs564474	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]
rs57588219	0.81[ASN][1000 genomes]
rs586159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs667911	0.83[ASN][1000 genomes]
rs678885	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681145	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248728	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7249730	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72623865	0.84[ASN][1000 genomes]
rs7508413	0.81[AFR][1000 genomes]
rs930100	0.85[CHB][hapmap];0.83[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs500660	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs500660	FBXO27	cis	Esophagus Mucosa	GTEx
rs500660	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs500660	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39480000-39503400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:39480200-39486600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:39481000-39516000	Weak transcription	Brain Angular Gyrus	brain
4	chr19:39481600-39484400	Enhancers	HMEC	breast
5	chr19:39481800-39484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:39482400-39484400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:39483000-39484400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:39483200-39484400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:39483200-39484600	Enhancers	NHEK	skin
10	chr19:39483200-39484800	Enhancers	HUVEC	blood vessel
11	chr19:39483400-39484400	Enhancers	Osteobl	bone
12	chr19:39483600-39484200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:39483600-39484200	Enhancers	Hela-S3	cervix
14	chr19:39483600-39484400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:39483600-39484400	Enhancers	NHDF-Ad	bronchial
16	chr19:39483800-39484000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:39483800-39484000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:39483800-39484000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr19:39483800-39484000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:39483800-39484000	Bivalent Enhancer	Esophagus	oesophagus
21	chr19:39483800-39484000	Enhancers	HSMM	muscle
22	chr19:39483800-39484200	Flanking Active TSS	A549	lung
23	chr19:39483800-39484200	Enhancers	HSMMtube	muscle
24	chr19:39483800-39484200	Enhancers	NH-A	brain
25	chr19:39483800-39484400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:39483800-39484400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:39483800-39484400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr19:39483800-39484400	Enhancers	GM12878-XiMat	blood

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