Variant report

Variant	rs1203936
Chromosome Location	chr20:22592430-22592431
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr20:22592336-22592596	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:22590072..22592802-chr20:22598328..22601056,2	MCF-7	breast:
2	chr20:22591562..22593117-chr20:22593356..22594890,2	MCF-7	breast:
3	chr20:22433807..22434458-chr20:22592270..22592916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237396	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1007202	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1007458	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146365	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1203920	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1203921	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203927	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1203928	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203929	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203930	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203931	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203932	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203933	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203935	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1203937	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203938	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203939	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203940	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203941	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203942	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203943	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203944	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203945	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203946	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203947	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203948	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203949	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203950	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1884742	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2180553	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2224316	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2424436	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424442	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424443	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2424444	0.87[EUR][1000 genomes]
rs6075931	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6082762	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6082765	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6137712	0.87[EUR][1000 genomes]
rs747911	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs747912	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754855	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs910956	0.86[EUR][1000 genomes]
rs910957	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs910960	0.85[EUR][1000 genomes]
rs995734	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1203936	FOXA2	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22591200-22594400	Enhancers	Stomach Mucosa	stomach
2	chr20:22592000-22593000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr20:22592200-22592600	Weak transcription	Gastric	stomach
4	chr20:22592200-22592800	Enhancers	H9 Cell Line	embryonic stem cell
5	chr20:22592200-22592800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr20:22592200-22592800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr20:22592400-22592600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr20:22592400-22592800	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr20:22592400-22592800	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr20:22592400-22593000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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