Variant report

Variant	rs12733015
Chromosome Location	chr1:58019733-58019734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11585229	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12564935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357785	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1357787	0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1404390	0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1539052	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1608691	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17116025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2185602	0.81[CEU][hapmap]
rs2691439	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2691461	0.95[CEU][hapmap];0.95[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793627	1.00[JPT][hapmap]
rs2793632	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2793633	0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2805847	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2805848	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2805852	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35023196	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7527457	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530027	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7541243	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1012555	chr1:57950355-58103389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv870802	chr1:57965114-58037031	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv523574	chr1:58018103-58087789	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12733015	GLIS1	cis	parietal	SCAN
rs12733015	MYSM1	cis	cerebellum	SCAN
rs12733015	C1orf177	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58015800-58020200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:58017600-58020000	Weak transcription	Stomach Mucosa	stomach
3	chr1:58017800-58019800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:58019200-58020200	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:58019400-58020000	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr1:58019400-58020000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:58019400-58020000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr1:58019400-58020000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr1:58019400-58020200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr1:58019600-58019800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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