Variant report

Variant	rs152963
Chromosome Location	chr5:97907617-97907618
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs152954	0.82[EUR][1000 genomes]
rs152955	0.83[EUR][1000 genomes]
rs152956	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs152957	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs152967	0.82[EUR][1000 genomes]
rs171528	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs181854	0.81[EUR][1000 genomes]
rs193500	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431067	0.81[EUR][1000 genomes]
rs251481	0.81[EUR][1000 genomes]
rs251482	0.81[EUR][1000 genomes]
rs251533	0.84[ASN][1000 genomes]
rs251535	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs25741	0.84[ASN][1000 genomes]
rs25742	0.84[ASN][1000 genomes]
rs27029	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27030	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27738	0.84[ASN][1000 genomes]
rs27786	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27870	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27971	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29661	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs29670	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29733	0.84[ASN][1000 genomes]
rs29734	0.84[ASN][1000 genomes]
rs29735	0.84[ASN][1000 genomes]
rs29736	0.84[ASN][1000 genomes]
rs36759	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36760	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36761	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36762	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36763	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36765	0.85[EUR][1000 genomes]
rs457020	0.81[EUR][1000 genomes]
rs460723	0.81[EUR][1000 genomes]
rs463369	0.81[EUR][1000 genomes]
rs466058	0.81[EUR][1000 genomes]
rs466259	0.81[EUR][1000 genomes]
rs467763	0.84[ASN][1000 genomes]
rs467853	0.80[EUR][1000 genomes]
rs468674	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs469191	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs469328	0.81[EUR][1000 genomes]
rs622487	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882412	chr5:97796120-97953719	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1016611	chr5:97873846-98035559	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv537816	chr5:97873846-98035559	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1029509	chr5:97888644-98040172	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs152963	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97905000-97908200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:97905000-97908400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:97906600-97912000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:97906800-97909000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr5:97906800-97910000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:97907000-97910000	Weak transcription	Fetal Intestine Large	intestine
7	chr5:97907400-97908400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:97907400-97909400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:97907400-97912400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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