Variant report

Variant	rs12144838
Chromosome Location	chr1:239619618-239619619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12117089	0.86[EUR][1000 genomes]
rs12117673	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12118163	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12118164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118522	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12119752	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12120600	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123857	0.81[JPT][hapmap]
rs12125436	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12128278	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12128683	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12136103	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12136673	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12138748	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12139749	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12141057	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12141123	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142001	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12142243	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12239665	0.85[EUR][1000 genomes]
rs16838380	0.85[EUR][1000 genomes]
rs17585014	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17645304	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60281676	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72754665	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754669	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72754672	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72754679	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72754702	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72756703	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7522967	0.84[EUR][1000 genomes]
rs946355	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs946356	0.93[AMR][1000 genomes];0.90[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	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	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
6	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
7	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:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239613200-239620400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:239614400-239625000	Weak transcription	Ovary	ovary
3	chr1:239617000-239619800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:239619600-239620200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links