Variant report

Variant	rs825456
Chromosome Location	chr12:124537575-124537576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10773049	0.89[ASN][1000 genomes]
rs10773050	0.89[ASN][1000 genomes]
rs10773051	0.90[ASN][1000 genomes]
rs10773052	0.90[ASN][1000 genomes]
rs10846583	0.90[ASN][1000 genomes]
rs10846584	0.94[ASN][1000 genomes]
rs10846585	0.96[ASN][1000 genomes]
rs10846586	0.94[ASN][1000 genomes]
rs11057425	0.96[ASN][1000 genomes]
rs12422529	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12579086	0.97[ASN][1000 genomes]
rs1387669	0.90[EUR][1000 genomes]
rs1686726	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1686755	0.90[EUR][1000 genomes]
rs1716394	0.88[EUR][1000 genomes]
rs1716407	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1996698	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451321	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2451322	0.91[EUR][1000 genomes]
rs2460761	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4765015	0.97[ASN][1000 genomes]
rs4765019	0.92[ASN][1000 genomes]
rs4765204	0.97[ASN][1000 genomes]
rs56962716	0.88[ASN][1000 genomes]
rs825452	0.89[ASN][1000 genomes]
rs825453	0.90[ASN][1000 genomes]
rs825455	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825458	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs825459	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs825461	0.85[EUR][1000 genomes]
rs825463	0.89[EUR][1000 genomes]
rs825465	0.85[EUR][1000 genomes]
rs825467	0.81[EUR][1000 genomes]
rs825473	0.84[EUR][1000 genomes]
rs825474	0.85[EUR][1000 genomes]
rs825475	0.85[EUR][1000 genomes]
rs825476	0.93[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs825477	0.81[EUR][1000 genomes]
rs825481	0.85[EUR][1000 genomes]
rs825482	0.85[EUR][1000 genomes]
rs825483	0.85[EUR][1000 genomes]
rs825484	0.84[EUR][1000 genomes]
rs825485	0.84[EUR][1000 genomes]
rs825486	0.85[EUR][1000 genomes]
rs825508	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs844085	0.85[EUR][1000 genomes]
rs851132	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs863750	1.00[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs825456	HNF1A	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124530600-124539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:124534600-124538200	Weak transcription	Fetal Kidney	kidney
3	chr12:124534600-124538400	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:124534600-124538400	Weak transcription	Stomach Mucosa	stomach
5	chr12:124534800-124538600	Weak transcription	Fetal Heart	heart
6	chr12:124536800-124538200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:124537200-124538400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:124537400-124537600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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