Variant report

Variant	rs12054976
Chromosome Location	chr5:45057320-45057321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12153053	0.81[AMR][1000 genomes]
rs4371761	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4533894	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56699889	0.90[AMR][1000 genomes]
rs59468706	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62369894	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62369895	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62369896	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62369905	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62369916	0.82[AMR][1000 genomes]
rs7701679	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7716101	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[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	nsv1027897	chr5:44695278-45061623	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1033740	chr5:44996257-45378556	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv537743	chr5:44996257-45378556	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1018651	chr5:45003750-45437670	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv537744	chr5:45003750-45437670	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv869151	chr5:45003751-45362364	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12054976	LOC647121	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:45056200-45057400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:45057000-45057600	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr5:45057000-45057600	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr5:45057000-45059400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:45057200-45059200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:45057200-45059400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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