Variant report

Variant	rs9846254
Chromosome Location	chr3:160770370-160770371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160768929..160771201-chr3:160940766..160943445,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10513560	0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10936216	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12496196	0.82[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs12690576	0.80[TSI][hapmap]
rs1374787	0.84[TSI][hapmap]
rs1447608	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1447609	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1530636	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1562465	0.91[CEU][hapmap];0.88[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1580253	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580254	0.97[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868109	0.82[TSI][hapmap]
rs2121721	0.92[CEU][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2889391	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34462546	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34884182	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35187206	0.86[AMR][1000 genomes]
rs6441345	0.88[CHB][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441346	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6763532	0.81[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6769927	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6770180	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6774203	0.92[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6791375	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6808311	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808386	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs733948	0.80[TSI][hapmap]
rs7613316	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7616249	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7635796	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7640874	0.92[CEU][hapmap]
rs7644586	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs898682	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9290065	0.81[MKK][hapmap]
rs9813700	0.85[EUR][1000 genomes]
rs9831488	0.81[MKK][hapmap]
rs9839984	0.94[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9840600	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857743	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs9858335	0.84[CHD][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860182	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873705	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9846254	PPM1L	cis	cerebellum	SCAN
rs9846254	TRIM59	cis	parietal	SCAN
rs9846254	C3orf57	cis	parietal	SCAN
rs9846254	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160745200-160782600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160768000-160778000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160768000-160786400	Weak transcription	Left Ventricle	heart
4	chr3:160769000-160770600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:160769200-160772400	Weak transcription	Right Ventricle	heart

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