Variant report

Variant	rs825463
Chromosome Location	chr12:124559697-124559698
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF664-1	chr12:124559470-124559839	XLOC_009925

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10846592	0.98[ASN][1000 genomes]
rs10846593	0.98[ASN][1000 genomes]
rs10846597	0.98[ASN][1000 genomes]
rs10846599	0.98[ASN][1000 genomes]
rs10846600	0.98[ASN][1000 genomes]
rs11057436	0.95[ASN][1000 genomes]
rs12422529	0.80[EUR][1000 genomes]
rs1387669	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1686726	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1686755	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1716394	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1716407	0.82[EUR][1000 genomes]
rs1996698	0.88[EUR][1000 genomes]
rs2451321	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451322	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460760	1.00[ASN][1000 genomes]
rs2460761	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61953589	0.89[ASN][1000 genomes]
rs7309216	0.98[ASN][1000 genomes]
rs825455	0.86[EUR][1000 genomes]
rs825456	0.89[EUR][1000 genomes]
rs825458	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs825459	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs825461	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs825465	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825467	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825473	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825474	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825475	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs825476	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs825477	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs825481	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825482	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825483	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825484	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs825485	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs825486	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs844085	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs851132	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124553800-124563200	Weak transcription	Stomach Mucosa	stomach
2	chr12:124554800-124560400	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr12:124556800-124560800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:124557600-124562200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:124558800-124559800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:124558800-124559800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:124558800-124560200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:124558800-124560400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:124558800-124560400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:124558800-124562000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:124558800-124562400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:124558800-124565200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:124559200-124560800	Enhancers	Fetal Intestine Large	intestine
14	chr12:124559600-124560600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:124559600-124571000	Weak transcription	Fetal Intestine Small	intestine

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