Variant report

Variant	rs12137225
Chromosome Location	chr1:239581298-239581299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12123857	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs12123979	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125061	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128683	0.85[ASN][1000 genomes]
rs12136118	0.87[ASN][1000 genomes]
rs12137093	0.87[ASN][1000 genomes]
rs12139749	0.82[ASN][1000 genomes]
rs12141057	0.81[ASN][1000 genomes]
rs2354402	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72754665	0.85[ASN][1000 genomes]
rs72754666	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72754668	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72754669	0.85[ASN][1000 genomes]
rs72754672	0.81[ASN][1000 genomes]
rs7548324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006640	chr1:239290853-239658788	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535358	chr1:239290853-239658788	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873349	chr1:239475925-239587512	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873350	chr1:239498915-239648140	Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr1:239570600-239581400	Weak transcription	Ovary	ovary
2	chr1:239572800-239581400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:239576600-239585000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:239576800-239583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239576800-239586800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:239577800-239581400	Weak transcription	Fetal Brain Female	brain
7	chr1:239578600-239581600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:239579200-239581400	Weak transcription	Fetal Brain Male	brain
9	chr1:239580200-239582200	Enhancers	Primary hematopoietic stem cells	blood
10	chr1:239580200-239582400	Enhancers	Colon Smooth Muscle	Colon
11	chr1:239581200-239581400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:239581200-239581600	Enhancers	Fetal Muscle Trunk	muscle
13	chr1:239581200-239582400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr1:239581200-239582400	Enhancers	Fetal Stomach	stomach
15	chr1:239581200-239582600	Enhancers	Rectal Smooth Muscle	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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