Variant report

Variant	rs4656481
Chromosome Location	chr1:166110922-166110923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10494453	0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs10494455	0.91[EUR][1000 genomes]
rs10800185	0.84[AMR][1000 genomes]
rs10800198	0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs10800199	0.89[EUR][1000 genomes]
rs10800200	0.90[EUR][1000 genomes]
rs10918369	0.88[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10918381	0.89[EUR][1000 genomes]
rs10918383	0.89[EUR][1000 genomes]
rs10918384	0.89[EUR][1000 genomes]
rs10918385	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12023523	0.89[EUR][1000 genomes]
rs12031538	0.93[EUR][1000 genomes]
rs12076837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12126834	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12136704	0.90[EUR][1000 genomes]
rs12144426	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12402371	0.89[EUR][1000 genomes]
rs12409766	0.89[EUR][1000 genomes]
rs12734750	0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs1432119	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1529642	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530889	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551179	0.86[EUR][1000 genomes]
rs1864791	0.89[EUR][1000 genomes]
rs2116519	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4074897	0.94[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4449996	0.85[AMR][1000 genomes]
rs4656484	0.89[EUR][1000 genomes]
rs4656485	0.89[EUR][1000 genomes]
rs4657530	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426968	0.91[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6681924	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696964	0.90[EUR][1000 genomes]
rs6698285	0.94[ASW][hapmap];0.90[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6698973	0.94[ASW][hapmap];0.91[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6700193	0.89[EUR][1000 genomes]
rs715421	0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs724139	0.89[EUR][1000 genomes]
rs7513325	0.88[ASW][hapmap];0.91[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7548172	0.92[EUR][1000 genomes]
rs9787101	0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs9787239	0.93[EUR][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	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4656481	PBX1	cis	cerebellum	SCAN
rs4656481	RCSD1	cis	parietal	SCAN
rs4656481	TIPRL	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166106200-166112400	Weak transcription	Psoas Muscle	Psoas
2	chr1:166106200-166119000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:166106600-166123200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:166109200-166119000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:166109400-166114600	Weak transcription	Spleen	Spleen
6	chr1:166109600-166111200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:166110000-166114400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:166110800-166111200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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