Variant report

Variant	rs13016636
Chromosome Location	chr2:31719147-31719148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1042578	0.83[JPT][hapmap]
rs11690596	0.83[JPT][hapmap]
rs12691180	0.80[EUR][1000 genomes]
rs12997020	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12997024	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13395648	0.83[JPT][hapmap]
rs13432696	0.82[AMR][1000 genomes]
rs17011453	0.83[JPT][hapmap]
rs1884722	1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs206798	0.92[JPT][hapmap]
rs206804	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs206805	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs206834	0.97[ASN][1000 genomes]
rs206836	0.97[ASN][1000 genomes]
rs206838	0.97[ASN][1000 genomes]
rs206841	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383032	0.96[AMR][1000 genomes]
rs28383050	0.96[AMR][1000 genomes]
rs35702549	0.80[EUR][1000 genomes]
rs3731586	0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs3754838	1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs472445	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494852	0.85[JPT][hapmap]
rs533833	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs541263	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6543634	0.83[JPT][hapmap]
rs7562326	1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs7594951	1.00[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs9332975	1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]

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
rs13016636	EIF2B4	cis	cerebellum	SCAN
rs13016636	CLIP4	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31712800-31719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:31718800-31719200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr2:31718800-31719200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr2:31718800-31719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:31718800-31719400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:31718800-31719600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:31718800-31719600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr2:31718800-31719600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:31718800-31719600	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:31718800-31719800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr2:31718800-31719800	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr2:31719000-31719200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:31719000-31719400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:31719000-31719600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr2:31719000-31719600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:31719000-31719600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr2:31719000-31719600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr2:31719000-31719600	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr2:31719000-31719600	Active TSS	K562	blood
20	chr2:31719000-31719600	Active TSS	NHEK	skin
21	chr2:31719000-31719800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:31719000-31719800	Active TSS	Placenta	Placenta

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