Variant report

Variant	rs4613331
Chromosome Location	chr2:30598568-30598569
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30545395..30547376-chr2:30598236..30600138,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514771	0.90[EUR][1000 genomes]
rs11127274	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11127275	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11885821	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11885871	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889918	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12468604	0.83[EUR][1000 genomes]
rs12471197	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12471227	0.83[EUR][1000 genomes]
rs12471481	0.83[EUR][1000 genomes]
rs12475327	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12988691	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12989601	0.90[EUR][1000 genomes]
rs13017527	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13029614	0.84[EUR][1000 genomes]
rs13034878	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357851	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34145247	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4572642	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375234	0.90[EUR][1000 genomes]
rs6706101	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6710587	0.84[EUR][1000 genomes]
rs6712757	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719566	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723368	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726574	0.84[EUR][1000 genomes]
rs6735708	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748329	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748436	0.88[EUR][1000 genomes]
rs6752411	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7599885	0.85[CEU][hapmap]
rs894787	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv873769	chr2:30585638-30625264	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4613331	DNAJC5G	cis	parietal	SCAN
rs4613331	TRIM54	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30585600-30605800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:30593000-30601000	Weak transcription	Pancreas	Pancrea
3	chr2:30597600-30599600	Weak transcription	Aorta	Aorta
4	chr2:30598200-30598600	Enhancers	Fetal Kidney	kidney

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