Variant report

Variant	rs153152
Chromosome Location	chr5:59842971-59842972
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC109486.1-1	chr5:59841929-59843484	ENSG00000152931
2	lnc-AC109486.1-1	chr5:59841929-59843465	XLOC_004399
3	lnc-AC109486.1-1	chr5:59841929-59843484	NONHSAT101637
4	lnc-AC109486.1-1	chr5:59841928-59843465	NONHSAT101641

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10058456	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10939855	0.80[EUR][1000 genomes]
rs10939856	0.82[EUR][1000 genomes]
rs10939860	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10939862	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11739724	0.83[ASN][1000 genomes]
rs11740327	1.00[CHB][hapmap]
rs11741754	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11948543	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs11951503	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11955398	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11959922	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs12514253	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12515025	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs12517174	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12517207	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12522801	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs1379114	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1379115	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1379116	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1456742	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1456743	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs1562235	0.82[ASN][1000 genomes]
rs17387940	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs1870014	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs2061250	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs206789	0.95[CHB][hapmap]
rs2198865	0.84[EUR][1000 genomes]
rs2409792	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs248911	1.00[ASN][1000 genomes]
rs248912	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249070	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26949	0.82[AFR][1000 genomes]
rs27564	0.84[ASN][1000 genomes]
rs286153	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs286154	1.00[CHB][hapmap]
rs286158	0.82[CHB][hapmap]
rs2898287	0.82[ASN][1000 genomes]
rs3857236	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs3958943	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4504343	0.82[EUR][1000 genomes]
rs4524466	0.83[CHB][hapmap]
rs4538566	0.82[EUR][1000 genomes]
rs4700378	0.80[ASN][1000 genomes]
rs55768631	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56137970	0.82[ASN][1000 genomes]
rs56166952	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56347749	0.82[EUR][1000 genomes]
rs59155887	0.84[EUR][1000 genomes]
rs62372964	0.80[ASN][1000 genomes]
rs62373023	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs755077	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7704338	0.85[CEU][hapmap]
rs7719611	0.85[CEU][hapmap]
rs7730342	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs9942410	0.83[CHB][hapmap];0.89[JPT][hapmap]

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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs153152	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs153152	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59838800-59844200	Weak transcription	Aorta	Aorta
2	chr5:59840600-59843000	Enhancers	Colon Smooth Muscle	Colon
3	chr5:59840600-59844600	Weak transcription	Hela-S3	cervix
4	chr5:59842000-59847200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr5:59842600-59847200	Weak transcription	Rectal Smooth Muscle	rectum

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