Variant report

Variant	rs2180553
Chromosome Location	chr20:22632419-22632420
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	chr20:22626256..22628397-chr20:22632199..22635114,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1007202	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1007458	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1146365	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1203920	0.87[EUR][1000 genomes]
rs1203921	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203925	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203927	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1203928	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203929	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203930	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203931	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203932	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203933	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203934	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1203935	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1203936	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1203937	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203938	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203939	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203940	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203941	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203942	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203943	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1203944	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203945	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203946	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203947	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1203948	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1203949	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1203950	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1543443	0.83[ASN][1000 genomes]
rs1884742	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2224316	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2424436	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2424442	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424443	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2424444	0.98[EUR][1000 genomes]
rs2424445	0.87[ASN][1000 genomes]
rs2424447	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2424448	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2424451	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4815129	0.89[EUR][1000 genomes]
rs6036172	0.83[ASN][1000 genomes]
rs6048241	0.83[ASN][1000 genomes]
rs6075931	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6075933	0.83[ASN][1000 genomes]
rs6075934	0.83[ASN][1000 genomes]
rs6082762	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6082765	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6082767	0.89[ASN][1000 genomes]
rs6082777	0.83[ASN][1000 genomes]
rs6113762	0.83[ASN][1000 genomes]
rs6137712	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73304706	0.83[ASN][1000 genomes]
rs747911	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs747912	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754855	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs910956	0.97[EUR][1000 genomes]
rs910957	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs910960	0.95[EUR][1000 genomes]
rs995734	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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	nsv428690	chr20:22528757-22649625	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1064571	chr20:22601105-22645251	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2180553	FOXA2	cis	Thyroid	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22630200-22633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:22632400-22634200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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