Variant report

Variant	rs361146
Chromosome Location	chr4:152889940-152889941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM160A1-5	chr4:152888148-152890531	XLOC_003737

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13129634	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1364870	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1425398	0.94[ASN][1000 genomes]
rs173405	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2020009	0.81[MEX][hapmap]
rs28429024	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360904	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360905	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360909	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs360911	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs360925	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360928	0.87[ASN][1000 genomes]
rs360934	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360935	0.88[ASN][1000 genomes]
rs360943	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360944	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360945	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360946	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360951	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360952	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs566370	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs578738	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6844372	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6845076	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879169	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9991939	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs361146	FGG	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152886600-152895800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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