Variant report

Variant	rs1654335
Chromosome Location	chr19:39482181-39482182
allele	A/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:

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]
rs12609745	0.83[ASN][1000 genomes]
rs12610086	0.81[ASN][1000 genomes]
rs13313727	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654334	0.84[AFR][1000 genomes]
rs1654336	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654337	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672656	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672657	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672659	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318956	0.82[AFR][1000 genomes]
rs473604	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482342	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483359	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490761	0.82[AFR][1000 genomes]
rs498586	0.95[ASN][1000 genomes]
rs500660	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500691	0.95[ASN][1000 genomes]
rs555858	0.94[ASN][1000 genomes]
rs55829324	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56111444	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563627	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs564474	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57588219	0.81[ASN][1000 genomes]
rs586159	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606372	0.83[AFR][1000 genomes]
rs62121526	0.87[ASN][1000 genomes]
rs622528	0.83[AFR][1000 genomes]
rs637972	0.91[AFR][1000 genomes]
rs650027	0.95[AFR][1000 genomes]
rs667911	0.83[ASN][1000 genomes]
rs678885	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681145	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248728	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7249730	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72623865	0.84[ASN][1000 genomes]
rs7508413	0.84[AFR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1654335	CTB-189B5.3	cis	Esophagus Mucosa	GTEx
rs1654335	CTB-189B5.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1654335	FBXO27	cis	Esophagus Mucosa	GTEx
rs1654335	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:32 , 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	chr19:39479600-39482800	Enhancers	Placenta	Placenta
3	chr19:39480000-39483800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr19:39480000-39503400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:39480200-39483800	Weak transcription	HSMMtube	muscle
6	chr19:39480200-39486600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:39480800-39482600	Bivalent Enhancer	HepG2	liver
8	chr19:39481000-39516000	Weak transcription	Brain Angular Gyrus	brain
9	chr19:39481400-39482200	Enhancers	Fetal Muscle Leg	muscle
10	chr19:39481600-39482200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:39481600-39482200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:39481600-39482200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39481600-39482200	Enhancers	Adipose Nuclei	Adipose
14	chr19:39481600-39482200	Enhancers	A549	lung
15	chr19:39481600-39482200	Enhancers	NHDF-Ad	bronchial
16	chr19:39481600-39482400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr19:39481600-39482400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr19:39481600-39482400	Enhancers	Osteobl	bone
19	chr19:39481600-39482600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:39481600-39484400	Enhancers	HMEC	breast
21	chr19:39481800-39482200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:39481800-39482200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:39481800-39482200	Enhancers	Hela-S3	cervix
24	chr19:39481800-39482200	Enhancers	HSMM	muscle
25	chr19:39481800-39482200	Bivalent Enhancer	NHLF	lung
26	chr19:39481800-39482400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:39481800-39482400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:39481800-39482400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:39481800-39482400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:39481800-39484600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:39482000-39482200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
32	chr19:39482000-39482200	Enhancers	HUVEC	blood vessel

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