Variant report

Variant	rs12088138
Chromosome Location	chr1:239679572-239679573
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10925903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925906	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807305	1.00[ASN][1000 genomes]
rs12058126	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12097468	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12240097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838358	0.92[ASN][1000 genomes]
rs16838359	0.92[ASN][1000 genomes]
rs16838363	0.92[ASN][1000 genomes]
rs20438	1.00[ASN][1000 genomes]
rs2354395	0.92[ASN][1000 genomes]
rs58291256	0.92[ASN][1000 genomes]
rs58463672	0.92[ASN][1000 genomes]
rs58716948	0.92[ASN][1000 genomes]
rs60374536	0.92[ASN][1000 genomes]
rs61595023	0.92[ASN][1000 genomes]
rs61834689	0.92[ASN][1000 genomes]
rs61834709	0.92[ASN][1000 genomes]
rs61834710	0.92[ASN][1000 genomes]
rs61834712	0.92[ASN][1000 genomes]
rs61834716	0.92[ASN][1000 genomes]
rs61834717	0.92[ASN][1000 genomes]
rs61834718	0.92[ASN][1000 genomes]
rs61834720	0.92[ASN][1000 genomes]
rs61834721	0.92[ASN][1000 genomes]
rs61834722	0.92[ASN][1000 genomes]
rs61834723	0.85[ASN][1000 genomes]
rs6661441	0.92[ASN][1000 genomes]
rs6666589	0.92[ASN][1000 genomes]
rs6669508	0.89[ASN][1000 genomes]
rs6675823	1.00[ASN][1000 genomes]
rs6681143	0.92[ASN][1000 genomes]
rs6693126	0.92[ASN][1000 genomes]
rs74149085	0.96[ASN][1000 genomes]
rs7513717	0.92[ASN][1000 genomes]
rs7517458	0.92[ASN][1000 genomes]
rs7519143	0.92[ASN][1000 genomes]
rs7549234	1.00[ASN][1000 genomes]
rs7551209	0.92[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	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	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
3	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
4	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239675600-239683600	Weak transcription	Pancreas	Pancrea
2	chr1:239676400-239679800	Weak transcription	Ovary	ovary
3	chr1:239678800-239679600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:239678800-239679600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:239678800-239679800	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:239678800-239680000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:239678800-239680000	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:239678800-239680200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:239679000-239680200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:239679400-239680000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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