Variant report

Variant	rs3917430
Chromosome Location	chr1:169695562-169695563
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1051091	0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs1076637	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1076638	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10919228	0.92[EUR][1000 genomes]
rs12027035	0.83[CEU][hapmap]
rs12072966	0.95[CHB][hapmap]
rs12076368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12079552	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087033	0.95[CHB][hapmap]
rs12131780	0.91[ASN][1000 genomes]
rs1883228	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.88[LWK][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs1883229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1961877	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2205847	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap];0.89[ASN][1000 genomes]
rs2205849	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2229569	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298899	0.95[CHB][hapmap]
rs2420503	0.89[ASN][1000 genomes]
rs28469136	0.92[EUR][1000 genomes]
rs35289447	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766129	0.95[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs3917423	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3917428	0.95[CHB][hapmap];0.82[MEX][hapmap]
rs3917432	0.95[CHB][hapmap]
rs3917435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427452	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656698	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656718	0.84[CHB][hapmap]
rs4987266	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4987298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4987301	0.95[CHB][hapmap];0.86[MEX][hapmap]
rs4987306	0.95[CHB][hapmap]
rs4987314	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap]
rs4987320	0.94[CHB][hapmap]
rs4987322	0.95[CHB][hapmap]
rs4987328	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap]
rs5356	0.85[CHB][hapmap];0.86[MEX][hapmap]
rs5359	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5368	0.84[CHB][hapmap];0.86[MEX][hapmap]
rs58662634	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59807249	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60277710	0.82[ASN][1000 genomes]
rs6427212	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7418242	0.95[CHB][hapmap]
rs7513119	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964555	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap]
rs964556	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap]
rs964557	0.91[ASW][hapmap];0.95[CHB][hapmap];0.86[MEX][hapmap]

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	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription 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	37 gene(s)	inside rSNPs	diseases
3	nsv872541	chr1:169672360-169695815	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3917430	FMO2	cis	cerebellum	SCAN
rs3917430	FMO3	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169691600-169698400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:169691800-169698200	Weak transcription	Left Ventricle	heart
3	chr1:169693800-169695800	Weak transcription	HepG2	liver
4	chr1:169694600-169696600	Flanking Active TSS	Liver	Liver
5	chr1:169695200-169696200	Enhancers	Rectal Mucosa Donor 31	rectum

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