Variant report

Variant	rs1168515
Chromosome Location	chr14:38835739-38835740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1168453	0.80[ASN][1000 genomes]
rs1168457	0.80[ASN][1000 genomes]
rs1168458	0.80[ASN][1000 genomes]
rs1168459	0.80[ASN][1000 genomes]
rs1168468	0.80[ASN][1000 genomes]
rs1168488	0.80[ASN][1000 genomes]
rs1168491	0.80[ASN][1000 genomes]
rs1168492	0.80[ASN][1000 genomes]
rs1168493	0.80[ASN][1000 genomes]
rs1168494	0.80[ASN][1000 genomes]
rs1168496	0.80[ASN][1000 genomes]
rs1168499	0.80[ASN][1000 genomes]
rs1168504	0.80[ASN][1000 genomes]
rs1168505	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168506	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1168507	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168508	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168509	0.80[ASN][1000 genomes]
rs1168510	0.80[ASN][1000 genomes]
rs1168512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168514	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168516	0.80[ASN][1000 genomes]
rs1168517	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168518	0.80[ASN][1000 genomes]
rs1168519	0.80[ASN][1000 genomes]
rs1168520	0.80[ASN][1000 genomes]
rs1183884	0.80[ASN][1000 genomes]
rs1183885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1184554	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1185623	0.80[ASN][1000 genomes]
rs990494	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916985	chr14:38052347-38838551	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
2	nsv533235	chr14:38558180-39117391	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv530640	chr14:38702117-38927901	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv901654	chr14:38822190-38870456	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2754119	chr14:38825349-38988849	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1168515	FOXA1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:38832600-38836800	Weak transcription	Psoas Muscle	Psoas
2	chr14:38835000-38835800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr14:38835000-38835800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:38835000-38835800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr14:38835400-38836200	Flanking Active TSS	HUVEC	blood vessel
6	chr14:38835600-38835800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:38835600-38835800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr14:38835600-38836000	Weak transcription	Gastric	stomach

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