Variant report

Variant	rs4656701
Chromosome Location	chr1:169687903-169687904
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1051091	0.94[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10800469	0.90[EUR][1000 genomes]
rs10919227	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12131780	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1883228	0.94[CEU][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2205847	0.94[CEU][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2420503	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3766129	0.94[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3917406	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs3917413	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3917436	1.00[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs3917444	0.94[EUR][1000 genomes]
rs3917449	0.87[EUR][1000 genomes]
rs4265482	0.82[EUR][1000 genomes]
rs4656189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656697	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4656703	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656704	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4786	1.00[CEU][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes]
rs4987270	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4987285	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4987318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5353	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs727909	0.94[EUR][1000 genomes]
rs932307	0.94[CEU][hapmap];0.92[TSI][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4656701	FMO2	cis	cerebellum	SCAN
rs4656701	KIFAP3	cis	parietal	SCAN
rs4656701	FMO3	cis	cerebellum	SCAN
rs4656701	METTL18	cis	Esophagus Mucosa	GTEx
rs4656701	METTL18	cis	lung	GTEx
rs4656701	ILDR2	cis	cerebellum	SCAN
rs4656701	METTL18	cis	Artery Tibial	GTEx
rs4656701	KIFAP3	cis	cerebellum	SCAN
rs4656701	POGK	cis	cerebellum	SCAN
rs4656701	METTL18	cis	Thyroid	GTEx
rs4656701	C1orf156	cis	parietal	SCAN
rs4656701	C1orf156	cis	cerebellum	SCAN
rs4656701	C1orf156	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169681200-169692000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:169681400-169691200	Weak transcription	Liver	Liver
3	chr1:169686400-169688200	ZNF genes & repeats	Dnd41	blood

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