Variant report

Variant	rs1018392
Chromosome Location	chr1:171353864-171353865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10157634	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1018390	0.87[ASN][1000 genomes]
rs1024171	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1024173	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912810	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10912830	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10912833	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10912842	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10912872	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11807475	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12057885	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12064618	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12121479	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12406999	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12564530	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12735239	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12736204	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12737633	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12739998	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12747017	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1963273	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2011345	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2011548	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2143090	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2179375	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2223477	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2235508	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2235509	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2235510	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2235511	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34668298	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35062585	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs36112567	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4615872	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4916225	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425167	0.82[EUR][1000 genomes]
rs6425192	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6425194	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6656117	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6656219	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6662297	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6667507	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6670432	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs6670627	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6688317	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6699676	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67595287	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7515001	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7516677	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7518648	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7519001	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7548166	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7555359	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs980120	0.82[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1002423	chr1:171294384-171376936	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv548188	chr1:171308832-171371998	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
7	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1018392	FMO4	cis	parietal	SCAN
rs1018392	PRDX6	cis	cerebellum	SCAN
rs1018392	FMO4	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171351600-171372600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:171353200-171354600	Enhancers	Fetal Intestine Small	intestine
3	chr1:171353200-171355000	Enhancers	Fetal Intestine Large	intestine

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