Variant report

Variant	rs55982339
Chromosome Location	chr3:54328329-54328330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12374075	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12374128	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3934631	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3934632	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3934633	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4078006	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4078007	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55715726	0.90[ASN][1000 genomes]
rs55725671	0.85[ASN][1000 genomes]
rs55751124	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55768606	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55777513	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55817503	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55826666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034762	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56198536	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56212431	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56271940	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56348221	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56352534	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56362821	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56411589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57211759	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57711599	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs57836319	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57897895	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57945354	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58976292	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59461034	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59804205	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59804657	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60855497	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61027914	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs61200778	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61444952	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62254145	0.81[ASN][1000 genomes]
rs62254148	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs62254157	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62254159	0.86[ASN][1000 genomes]
rs62256086	0.84[EUR][1000 genomes]
rs6445640	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445641	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6445643	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6445644	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6781457	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6790114	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7427601	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7428097	0.86[ASN][1000 genomes]
rs7428562	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7428712	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7430091	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7432978	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7433995	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7434141	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7434171	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7615455	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7622924	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7645884	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7649860	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9714322	0.86[EUR][1000 genomes]
rs9883365	0.84[EUR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876806	chr3:54256648-54330010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region 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	chr3:54328000-54328600	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr3:54328200-54328600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:54328200-54328800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr3:54328200-54328800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links