Variant report

Variant	rs12142230
Chromosome Location	chr1:90865496-90865497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10922854	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12119538	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12124677	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12126859	0.96[ASN][1000 genomes]
rs12127465	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12129462	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12136436	0.88[EUR][1000 genomes]
rs12136957	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12137705	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1396317	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1396318	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61770072	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532588	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000787	chr1:90809476-90874481	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv3394726	chr1:90811671-91019675	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1801569	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv1808806	chr1:90819992-90983299	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv1822918	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv1850863	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2757740	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2758949	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv427697	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv428124	chr1:90819992-90983299	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv1811797	chr1:90819992-91008105	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv432487	chr1:90824652-90931765	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:90854400-90868200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:90863600-90868200	Weak transcription	HUVEC	blood vessel
3	chr1:90863800-90880200	Weak transcription	Aorta	Aorta
4	chr1:90865200-90866000	Enhancers	Hela-S3	cervix
5	chr1:90865200-90869000	Enhancers	Stomach Mucosa	stomach
6	chr1:90865400-90865800	Enhancers	Gastric	stomach
7	chr1:90865400-90865800	Flanking Active TSS	NHEK	skin
8	chr1:90865400-90866200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:90865400-90866200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:90865400-90866200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:90865400-90869200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:90865400-90869400	Enhancers	HMEC	breast

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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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