Variant report

Variant	rs7545923
Chromosome Location	chr1:171148721-171148722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10157270	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10489230	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798240	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798253	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10798263	0.95[JPT][hapmap]
rs10912475	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912529	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10912537	0.95[JPT][hapmap]
rs10912542	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912552	0.95[JPT][hapmap]
rs11806072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12069067	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12078953	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12080576	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12090485	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12133385	0.88[ASN][1000 genomes]
rs12402693	1.00[YRI][hapmap]
rs12405613	0.88[ASN][1000 genomes]
rs12566823	0.95[JPT][hapmap]
rs12567956	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12730305	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12744605	0.80[AMR][1000 genomes]
rs16863990	1.00[YRI][hapmap]
rs17350523	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1989656	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2008706	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2020862	0.95[JPT][hapmap]
rs2049922	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2064078	0.90[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2075987	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075990	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075991	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[ASN][1000 genomes]
rs2179105	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2205723	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2205724	0.95[JPT][hapmap]
rs2205727	0.86[ASN][1000 genomes]
rs2205728	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2205729	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2223228	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2223232	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2236874	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2421709	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2421710	0.88[ASN][1000 genomes]
rs2421711	0.88[ASN][1000 genomes]
rs35152982	0.87[ASN][1000 genomes]
rs3738813	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3754489	1.00[YRI][hapmap]
rs3754494	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3754495	0.83[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs3768569	0.95[JPT][hapmap]
rs3768570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4480395	0.84[ASN][1000 genomes]
rs4916182	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4916191	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4916192	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6425394	0.90[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425413	0.88[ASN][1000 genomes]
rs6657314	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672029	0.86[ASN][1000 genomes]
rs6692260	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692347	0.95[JPT][hapmap]
rs6699803	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6701076	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6703439	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7513485	0.88[ASN][1000 genomes]
rs7520777	0.85[ASN][1000 genomes]
rs7524635	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7525342	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529080	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7531713	0.84[ASN][1000 genomes]
rs7531971	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7536822	0.88[ASN][1000 genomes]
rs7538013	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553869	0.84[ASN][1000 genomes]
rs7887505	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs926268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7545923	RP1-127D3.4	cis	Artery Tibial	GTEx
rs7545923	FMO2	cis	parietal	SCAN
rs7545923	FMO2	cis	Artery Tibial	GTEx
rs7545923	FMO3	cis	cerebellum	SCAN
rs7545923	FMO2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171143800-171153200	Weak transcription	Fetal Lung	lung
2	chr1:171148200-171153400	Weak transcription	Aorta	Aorta
3	chr1:171148600-171149200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:171148600-171150000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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