Variant report

Variant	rs541263
Chromosome Location	chr2:31729141-31729142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1042578	0.91[JPT][hapmap]
rs11690596	0.91[JPT][hapmap]
rs13016636	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13395648	0.91[JPT][hapmap]
rs17011453	0.91[JPT][hapmap]
rs1884722	0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs206798	0.84[JPT][hapmap]
rs206804	0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs206805	0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs206834	0.92[ASN][1000 genomes]
rs206836	0.92[ASN][1000 genomes]
rs206838	0.92[ASN][1000 genomes]
rs206841	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs206844	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3731586	0.91[JPT][hapmap]
rs3754838	0.86[GIH][hapmap];0.91[JPT][hapmap]
rs472445	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533833	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6543634	0.91[JPT][hapmap]
rs7562326	0.86[GIH][hapmap];0.91[JPT][hapmap]
rs7594951	0.86[GIH][hapmap];0.91[JPT][hapmap]
rs9332975	0.86[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv999815	chr2:31654667-31777296	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv2664	chr2:31710417-31733762	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs541263	EIF2B4	cis	cerebellum	SCAN
rs541263	CLIP4	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31727600-31730800	Enhancers	Fetal Intestine Large	intestine
2	chr2:31727600-31731600	Enhancers	Fetal Intestine Small	intestine
3	chr2:31728600-31730200	Enhancers	Duodenum Mucosa	Duodenum
4	chr2:31729000-31729200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:31729000-31729200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr2:31729000-31730400	Enhancers	Stomach Mucosa	stomach

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