Variant report

Variant	rs1532423
Chromosome Location	chr8:86268313-86268314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10087278	0.89[ASN][1000 genomes]
rs10090196	0.86[JPT][hapmap]
rs10091566	0.88[ASN][1000 genomes]
rs10095352	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10097917	0.85[ASN][1000 genomes]
rs10504812	1.00[JPT][hapmap]
rs10504813	0.95[JPT][hapmap]
rs10907474	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11261471	0.82[JPT][hapmap]
rs11261474	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11985029	0.88[ASN][1000 genomes]
rs11985733	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12541445	0.82[JPT][hapmap]
rs12544332	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12550814	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1303806	0.91[JPT][hapmap]
rs13252971	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs13255540	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13259399	0.86[JPT][hapmap]
rs13273654	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389245	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1389247	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1390711	0.91[JPT][hapmap]
rs1390712	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1472360	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1493302	0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1496526	0.88[ASN][1000 genomes]
rs1496529	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1496530	0.95[JPT][hapmap]
rs1496531	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1496532	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1532424	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1543852	0.88[ASN][1000 genomes]
rs1553015	0.91[JPT][hapmap]
rs16913721	0.86[JPT][hapmap]
rs17042	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1908075	0.86[ASN][1000 genomes]
rs1995056	0.86[JPT][hapmap]
rs1995057	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1995058	0.91[JPT][hapmap]
rs2006767	0.86[JPT][hapmap]
rs2055077	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs20571	0.86[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2072696	0.95[JPT][hapmap]
rs2173044	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278459	0.82[JPT][hapmap]
rs2279701	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2291787	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2307075	0.84[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2403104	0.91[JPT][hapmap]
rs2403105	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2453868	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2548281	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2645047	0.88[ASN][1000 genomes]
rs2645049	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2645053	0.84[ASN][1000 genomes]
rs2896452	0.82[JPT][hapmap]
rs3087782	1.00[JPT][hapmap]
rs3758076	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs3758078	0.80[CEU][hapmap];0.90[JPT][hapmap];0.85[TSI][hapmap]
rs3808538	0.86[JPT][hapmap]
rs3808539	0.91[JPT][hapmap]
rs4150942	0.82[JPT][hapmap]
rs4566	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs4739700	0.86[JPT][hapmap]
rs4740044	0.86[JPT][hapmap]
rs4740049	0.91[JPT][hapmap]
rs6605611	0.81[CHB][hapmap]
rs66498753	0.84[ASN][1000 genomes]
rs6988475	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs6990449	0.81[JPT][hapmap]
rs6993387	0.86[JPT][hapmap]
rs6997458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7000950	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7001359	0.82[JPT][hapmap]
rs7008772	0.86[JPT][hapmap]
rs7011926	0.91[JPT][hapmap]
rs7016369	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs713488	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs713489	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs725605	0.83[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7818163	0.86[JPT][hapmap]
rs7824715	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs903895	0.91[JPT][hapmap]
rs903896	0.91[JPT][hapmap]
rs903897	0.91[JPT][hapmap]
rs931505	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9969643	0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs9987281	0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]

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	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1024759	chr8:86162507-86361533	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv539659	chr8:86162507-86361533	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv971674	chr8:86187966-86338484	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1022463	chr8:86257031-86547831	Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1804888	chr8:86263098-86986703	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv831377	chr8:86263107-86444141	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood trace element (Zn levels)	23720494	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1532423	C8orf59	cis	cerebellum	SCAN
rs1532423	LRRCC1	cis	Esophagus Mucosa	GTEx
rs1532423	RALYL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86265200-86283200	Weak transcription	Fetal Intestine Large	intestine
2	chr8:86265400-86278000	Weak transcription	Fetal Intestine Small	intestine
3	chr8:86267400-86270800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:86267400-86270800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:86267400-86270800	Weak transcription	K562	blood
6	chr8:86267400-86271000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr8:86267400-86275400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr8:86267400-86288800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr8:86267600-86270800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr8:86267600-86271000	Weak transcription	HMEC	breast
11	chr8:86267600-86271000	Weak transcription	NHEK	skin
12	chr8:86267600-86271200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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