Variant report

Variant	rs825461
Chromosome Location	chr12:124561803-124561804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10846592	0.98[ASN][1000 genomes]
rs10846593	0.98[ASN][1000 genomes]
rs10846597	0.98[ASN][1000 genomes]
rs10846599	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10846600	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs11057436	0.95[ASN][1000 genomes]
rs1387669	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1686726	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1686755	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1716394	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1716407	0.88[CEU][hapmap]
rs1996698	0.85[EUR][1000 genomes]
rs2451321	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451322	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460760	1.00[ASN][1000 genomes]
rs2460761	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953589	0.89[ASN][1000 genomes]
rs7309216	0.98[ASN][1000 genomes]
rs825455	0.82[EUR][1000 genomes]
rs825456	0.85[EUR][1000 genomes]
rs825458	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs825459	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs825463	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825465	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825467	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825473	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825474	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825475	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825476	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825477	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs825481	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825482	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825483	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825484	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs825485	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825486	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs844085	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851132	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899580	chr12:124499542-124565258	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv455734	chr12:124511908-124772515	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv560538	chr12:124511908-124772515	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv520633	chr12:124548394-124683205	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv523233	chr12:124561803-124565258	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv518962	chr12:124561803-124583446	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs825461	HNF1A	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124553800-124563200	Weak transcription	Stomach Mucosa	stomach
2	chr12:124557600-124562200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:124558800-124562000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:124558800-124562400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:124558800-124565200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:124559600-124571000	Weak transcription	Fetal Intestine Small	intestine
7	chr12:124560400-124562600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:124560800-124562000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:124561800-124562600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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