Variant report

Variant	rs374613
Chromosome Location	chr5:112192072-112192073
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	chr5:112191204..112194360-chr5:112195263..112198616,8	MCF-7	breast:
2	chr5:112180694..112183270-chr5:112188278..112192219,3	K562	blood:

Variant related genes	Relation type
ENSG00000153037	Chromatin interaction
ENSG00000272869	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10075281	0.84[ASW][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs1093611	0.90[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs11241182	0.84[ASW][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap]
rs11241185	0.84[ASW][hapmap];0.81[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs12518091	0.85[CEU][hapmap]
rs149130	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs149190	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs149192	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs149193	0.82[EUR][1000 genomes]
rs1530256	0.84[CHB][hapmap]
rs153544	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[EUR][1000 genomes]
rs153546	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs153548	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs153549	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs153550	0.85[ASN][1000 genomes]
rs153551	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs153552	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154344	0.83[EUR][1000 genomes]
rs17135222	0.82[TSI][hapmap]
rs1866924	0.81[CHD][hapmap];0.83[TSI][hapmap]
rs1914	0.81[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1968557	0.84[CHB][hapmap]
rs1974786	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs2019720	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs2229992	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2289484	0.84[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs2431241	0.81[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs2431512	0.84[ASW][hapmap];0.85[CEU][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs2439595	0.89[CHB][hapmap]
rs2464803	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs2545155	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2545156	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545170	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2546106	0.84[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs2546108	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs2546110	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap]
rs2546112	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2546115	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs2546117	0.85[CHB][hapmap]
rs2707763	0.84[CHB][hapmap]
rs2707765	0.81[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs3317	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs351767	0.90[ASN][1000 genomes]
rs351768	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351770	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs351772	0.81[AMR][1000 genomes]
rs368575	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs373059	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs382427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs390092	0.93[JPT][hapmap]
rs395858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs396321	0.84[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs410701	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41116	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs414098	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap]
rs419155	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs448162	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.94[ASN][1000 genomes]
rs448475	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs448613	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454886	0.84[CHB][hapmap]
rs454968	0.95[ASN][1000 genomes]
rs456531	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs459102	0.87[ASN][1000 genomes]
rs460137	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs467033	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap]
rs468751	0.82[EUR][1000 genomes]
rs468854	0.81[ASN][1000 genomes]
rs469827	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs469886	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[EUR][1000 genomes]
rs4705486	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs4705559	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs4705608	0.85[CEU][hapmap];0.84[CHB][hapmap]
rs4705610	0.84[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4705624	0.89[CHB][hapmap]
rs495794	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs505382	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514763	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs566419	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6594646	0.84[ASW][hapmap];0.85[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs67293732	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6862050	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs712663	0.86[ASN][1000 genomes]
rs712670	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7213	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs7704618	0.85[CEU][hapmap]
rs818426	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs818428	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818429	0.87[ASN][1000 genomes]
rs818430	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs818797	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9326863	0.84[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032464	chr5:112076061-112192380	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv537862	chr5:112076061-112192380	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv33290	chr5:112110808-112238295	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1034239	chr5:112161239-112194693	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv529536	chr5:112174106-112269758	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs374613	REEP5	cis	multi-tissue	Pritchard
rs374613	NCRNA00219	cis	parietal	SCAN
rs374613	REEP5	cis	cerebellum	SCAN
rs374613	REEP5	cis	Liver	GTEx
rs374613	MCC	cis	cerebellum	SCAN
rs374613	REEP5	cis	uninvolved skin	skin_eQTL
rs374613	REEP5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112189400-112196200	Weak transcription	Spleen	Spleen
2	chr5:112191400-112196400	Weak transcription	HepG2	liver
3	chr5:112191600-112192400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:112191600-112192600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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