Variant report

Variant	rs1203949
Chromosome Location	chr20:22605697-22605698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-10	chr20:22604710-22606895	NONHSAT079002
2	lnc-FOXA2-10	chr20:22604710-22606895	ucscGeneNc_uc002wso_1

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1007202	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1007458	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1146365	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1203920	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1203921	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203925	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203927	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1203928	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203929	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203930	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203931	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203932	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203933	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203934	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203935	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1203936	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203937	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203938	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203939	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203940	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203941	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203942	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203943	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203944	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203945	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203946	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203947	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203950	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1884742	0.87[EUR][1000 genomes]
rs2180553	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2224316	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424436	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424442	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424443	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2424444	0.88[EUR][1000 genomes]
rs4815129	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6075931	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6082762	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6082765	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6137712	0.86[EUR][1000 genomes]
rs747911	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs747912	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs754855	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs910956	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs910957	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs910960	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs995734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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
rs1203949	FOXA2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22601600-22607200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:22603800-22611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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