Variant report

Variant	rs12617160
Chromosome Location	chr2:114414087-114414088
allele	C/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	FOXA2	chr2:114413686-114414514	A549	lung:	n/a	n/a
2	FOXA2	chr2:114413910-114414311	A549	lung:	n/a	n/a
3	FOXA1	chr2:114413904-114414220	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000144158	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11677238	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57435814	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759085	chr2:114074949-114428678	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
2	nsv428062	chr2:114251945-114428678	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	esv2757827	chr2:114253780-114428678	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv1001195	chr2:114362003-114506330	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv508163	chr2:114364609-114431004	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv961495	chr2:114381866-114415806	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv962001	chr2:114390234-114415806	Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs12617160	DDX11L2	cis	Esophagus Mucosa	GTEx
rs12617160	RPL23AP7	cis	Muscle Skeletal	GTEx
rs12617160	DDX11L2	cis	Nerve Tibial	GTEx
rs12617160	RPL23AP7	cis	Esophagus Mucosa	GTEx
rs12617160	RPL23AP7	Cis_1M	lymphoblastoid	RTeQTL
rs12617160	DDX11L2	cis	Stomach	GTEx
rs12617160	DDX11L2	cis	Artery Tibial	GTEx
rs12617160	DDX11L2	cis	Whole Blood	GTEx
rs12617160	RP11-395L14.5	cis	Adipose Subcutaneous	GTEx
rs12617160	RPL23AP7	cis	Adipose Subcutaneous	GTEx
rs12617160	RPL23AP7	cis	Artery Aorta	GTEx
rs12617160	DDX11L2	cis	Artery Aorta	GTEx
rs12617160	DDX11L2	cis	Muscle Skeletal	GTEx
rs12617160	RPL23AP7	cis	Esophagus Muscularis	GTEx
rs12617160	DDX11L2	cis	Thyroid	GTEx
rs12617160	DDX11L2	cis	Skin Sun Exposed Lower leg	GTEx
rs12617160	RPL23AP7	cis	Artery Tibial	GTEx
rs12617160	DDX11L2	cis	lung	GTEx
rs12617160	DDX11L2	cis	Heart Left Ventricle	GTEx
rs12617160	DDX11L2	cis	Esophagus Muscularis	GTEx
rs12617160	RPL23AP7	cis	Whole Blood	GTEx
rs12617160	RPL23AP7	cis	lung	GTEx
rs12617160	DDX11L2	cis	Adipose Subcutaneous	GTEx
rs12617160	RP11-395L14.5	cis	Artery Tibial	GTEx
rs12617160	RPL23AP7	cis	Heart Left Ventricle	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114413400-114414200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr2:114413400-114414200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
3	chr2:114413400-114414200	Active TSS	A549	lung
4	chr2:114413400-114414200	Active TSS	HepG2	liver
5	chr2:114413600-114414200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:114413600-114414200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr2:114413600-114414200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr2:114413600-114414200	Active TSS	K562	blood
9	chr2:114413800-114414200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr2:114413800-114414200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:114413800-114414200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:114413800-114414200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:114413800-114414200	Active TSS	Rectal Mucosa Donor 29	rectum

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