Variant report

Variant	rs498586
Chromosome Location	chr19:39484081-39484082
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:
2	chr19:39478331..39480125-chr19:39483725..39485536,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269190	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10409280	0.81[JPT][hapmap]
rs12609745	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610086	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13313727	0.80[JPT][hapmap];0.95[ASN][1000 genomes]
rs1627631	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1628376	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1654335	0.95[ASN][1000 genomes]
rs1654336	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1654337	0.95[ASN][1000 genomes]
rs1672656	0.94[ASN][1000 genomes]
rs1672657	0.93[ASN][1000 genomes]
rs1672658	0.95[ASN][1000 genomes]
rs1672659	0.95[ASN][1000 genomes]
rs16973058	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17795157	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs473604	0.95[ASN][1000 genomes]
rs482342	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs483359	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs500660	0.84[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs500691	1.00[CEU][hapmap];1.00[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]
rs523943	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs555858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55829324	0.95[ASN][1000 genomes]
rs56111444	0.95[ASN][1000 genomes]
rs563627	0.91[ASN][1000 genomes]
rs564474	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs57038019	0.86[EUR][1000 genomes]
rs572764	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs57588219	0.83[ASN][1000 genomes]
rs582575	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs582593	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs583529	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs583995	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs584806	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs586159	0.95[ASN][1000 genomes]
rs61091122	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62121526	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs662202	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs667911	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs678772	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs678885	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs681145	0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7248728	0.86[ASN][1000 genomes]
rs7249730	0.85[ASN][1000 genomes]
rs72623865	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs930100	0.81[JPT][hapmap]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs498586	FBXO27	cis	Liver	GTEx
rs498586	OPA3	cis	cerebellum	SCAN
rs498586	ZNF45	cis	parietal	SCAN
rs498586	DYRK1B	cis	cerebellum	SCAN
rs498586	ZNF576	cis	cerebellum	SCAN
rs498586	FBXO27	cis	multi-tissue	Pritchard
rs498586	ZNF526	cis	parietal	SCAN

Chromatin state (count:24 , 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	chr19:39483800-39484200	Flanking Active TSS	A549	lung
17	chr19:39483800-39484200	Enhancers	HSMMtube	muscle
18	chr19:39483800-39484200	Enhancers	NH-A	brain
19	chr19:39483800-39484400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr19:39483800-39484400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:39483800-39484400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr19:39483800-39484400	Enhancers	GM12878-XiMat	blood
23	chr19:39484000-39484200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:39484000-39484400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin

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