Variant report

Variant	rs58827878
Chromosome Location	chr5:178481936-178481937
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10479519	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10479520	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10516149	0.90[ASN][1000 genomes]
rs10516150	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11951738	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11957976	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11958355	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11960161	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152869	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13160086	0.81[ASN][1000 genomes]
rs13161528	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13188724	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13359549	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13359570	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13359572	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13361077	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17078988	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17078991	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2047354	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132671	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132672	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34054398	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34431447	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34881171	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35568336	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3797615	0.82[ASN][1000 genomes]
rs4700780	0.88[ASN][1000 genomes]
rs4700781	0.83[ASN][1000 genomes]
rs4701030	0.90[ASN][1000 genomes]
rs4701045	0.82[ASN][1000 genomes]
rs60061283	0.84[ASN][1000 genomes]
rs60073676	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62393072	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62393074	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62393075	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62393076	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601007	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859576	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6859767	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6860309	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6861539	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6867119	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6867208	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6868893	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6875473	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6875622	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6880315	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6888539	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6888567	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890317	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7707587	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7708743	0.87[ASN][1000 genomes]
rs7709054	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7711420	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732719	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7733072	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027487	chr5:178455495-178510587	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58827878	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178479600-178482200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:178481000-178483600	Enhancers	Placenta Amnion	Placenta Amnion
3	chr5:178481400-178483600	Enhancers	Placenta	Placenta
4	chr5:178481600-178482600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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