Variant report

Variant	rs12474091
Chromosome Location	chr2:12225176-12225177
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10183374	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10190465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12997170	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62113831	0.91[ASN][1000 genomes]
rs7419959	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv997538	chr2:12216408-12242734	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	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
rs12474091	AC012456.4	cis	Nerve Tibial	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12217400-12249800	Weak transcription	GM12878-XiMat	blood
2	chr2:12221000-12234200	Weak transcription	Spleen	Spleen
3	chr2:12223400-12227000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr2:12223600-12225200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:12223800-12227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:12224000-12226000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:12224000-12227400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:12224200-12225200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:12224400-12226200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:12224400-12230800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:12224600-12236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:12224800-12225600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:12224800-12225600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:12224800-12227000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:12224800-12229600	Weak transcription	Brain Germinal Matrix	brain
16	chr2:12224800-12238000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:12225000-12225400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr2:12225000-12225400	Weak transcription	iPS-20b 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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