Variant report

Variant	rs12039269
Chromosome Location	chr1:221973437-221973438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10495178	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11118858	0.82[JPT][hapmap]
rs12022218	0.81[EUR][1000 genomes]
rs12026940	0.81[EUR][1000 genomes]
rs12030246	0.81[EUR][1000 genomes]
rs12034339	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12036282	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs12038356	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041329	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17010785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3003901	0.81[EUR][1000 genomes]
rs58234964	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58787358	0.85[EUR][1000 genomes]
rs6680297	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6680316	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6680505	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72629678	0.81[EUR][1000 genomes]
rs7532339	0.88[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs9441946	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv947161	chr1:221967491-221977571	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv945668	chr1:221968101-221974035	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12039269	hmm26268	cis	multi-tissue	Pritchard
rs12039269		cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221967400-222009800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:221968000-221974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:221968600-221974200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:221971200-221975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:221973400-221974600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:221973400-221979800	Weak transcription	Primary B cells from cord blood	blood

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Input of quick search could be:

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

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