Variant report

Variant	rs293409
Chromosome Location	chr4:69601023-69601024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1454254	0.86[EUR][1000 genomes]
rs186053	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs293408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293445	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs293467	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4148263	0.81[EUR][1000 genomes]
rs6854768	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv870075	chr4:69218674-69608683	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1005513	chr4:69446718-69890307	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv2763366	chr4:69592847-69661427	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1013885	chr4:69592847-69667996	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829961	chr4:69592847-69695467	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv594579	chr4:69597175-69665970	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1014042	chr4:69599853-69667996	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs293409	TMPRSS11A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69599000-69603000	Enhancers	Rectal Mucosa Donor 31	rectum
2	chr4:69599200-69602800	Enhancers	Stomach Mucosa	stomach
3	chr4:69599800-69601200	Active TSS	Fetal Stomach	stomach
4	chr4:69600000-69602800	Enhancers	Fetal Intestine Small	intestine
5	chr4:69600400-69601600	Enhancers	Liver	Liver
6	chr4:69600600-69601400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:69600800-69601200	Flanking Active TSS	Fetal Intestine Large	intestine
8	chr4:69600800-69602200	Weak transcription	Fetal Kidney	kidney
9	chr4:69600800-69602200	Enhancers	Pancreas	Pancrea
10	chr4:69600800-69602200	Enhancers	Small Intestine	intestine
11	chr4:69600800-69603800	Enhancers	HepG2	liver
12	chr4:69601000-69601200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr4:69601000-69601200	Enhancers	Gastric	stomach
14	chr4:69601000-69601400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:69601000-69602400	Weak transcription	A549	lung

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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