Variant report

Variant	rs1497000
Chromosome Location	chr4:44926711-44926712
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10000940	0.81[EUR][1000 genomes]
rs10001739	0.81[EUR][1000 genomes]
rs10003579	0.80[EUR][1000 genomes]
rs10003776	0.81[EUR][1000 genomes]
rs10003984	0.81[EUR][1000 genomes]
rs10004173	0.81[EUR][1000 genomes]
rs10006643	0.81[EUR][1000 genomes]
rs10031439	0.81[EUR][1000 genomes]
rs10034588	0.81[EUR][1000 genomes]
rs10433683	0.82[EUR][1000 genomes]
rs10433684	0.82[EUR][1000 genomes]
rs10461061	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938372	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10938378	0.81[EUR][1000 genomes]
rs11726237	0.81[EUR][1000 genomes]
rs11727488	0.81[EUR][1000 genomes]
rs11730391	0.81[EUR][1000 genomes]
rs12501461	0.81[EUR][1000 genomes]
rs12502784	0.81[EUR][1000 genomes]
rs12503075	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12504288	0.81[EUR][1000 genomes]
rs12505440	0.80[EUR][1000 genomes]
rs12512128	0.81[EUR][1000 genomes]
rs12512173	0.81[EUR][1000 genomes]
rs12513234	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13123198	0.81[EUR][1000 genomes]
rs13125752	0.81[EUR][1000 genomes]
rs13145245	0.81[EUR][1000 genomes]
rs1390915	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1390923	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1497003	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948587	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28712193	0.82[EUR][1000 genomes]
rs2882027	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34398887	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34625281	0.81[EUR][1000 genomes]
rs35739449	0.80[EUR][1000 genomes]
rs4264865	0.83[EUR][1000 genomes]
rs4267770	0.81[EUR][1000 genomes]
rs4447894	0.81[EUR][1000 genomes]
rs4456993	0.80[EUR][1000 genomes]
rs4464602	0.81[EUR][1000 genomes]
rs4467605	0.81[EUR][1000 genomes]
rs4481265	0.81[EUR][1000 genomes]
rs4492035	0.81[CEU][hapmap]
rs4558900	0.81[EUR][1000 genomes]
rs4560452	0.81[EUR][1000 genomes]
rs4621472	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4635847	0.81[EUR][1000 genomes]
rs4639112	0.81[EUR][1000 genomes]
rs4695069	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs5002959	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820860	0.81[EUR][1000 genomes]
rs6822744	0.81[EUR][1000 genomes]
rs6823446	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6828498	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832190	0.80[EUR][1000 genomes]
rs6848088	0.81[EUR][1000 genomes]
rs6848089	0.81[EUR][1000 genomes]
rs6855537	0.80[EUR][1000 genomes]
rs7655634	0.83[EUR][1000 genomes]
rs7657077	0.83[EUR][1000 genomes]
rs7658399	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7677319	0.82[EUR][1000 genomes]
rs7678059	0.82[EUR][1000 genomes]
rs7682854	0.82[EUR][1000 genomes]
rs7698277	0.82[EUR][1000 genomes]
rs7699473	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531944	chr4:44299343-45200700	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1013488	chr4:44543808-44976123	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv915992	chr4:44705614-44972966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1014327	chr4:44735209-45218149	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878979	chr4:44871931-45102488	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv432591	chr4:44922068-45017576	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1497000	GNPDA2	cis	cerebellum	SCAN
rs1497000	TMEM33	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:44919200-44928400	Weak transcription	Psoas Muscle	Psoas
2	chr4:44921000-44928800	Weak transcription	Fetal Heart	heart

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