Variant report

Variant	rs4616689
Chromosome Location	chr3:160856269-160856270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1026572	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs1037888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513559	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap]
rs10513562	0.89[CEU][hapmap]
rs10936223	0.83[EUR][1000 genomes]
rs1154701	1.00[JPT][hapmap]
rs12493960	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12631850	0.84[EUR][1000 genomes]
rs13066683	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13098884	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1382427	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1478565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1599374	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599376	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599378	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1599379	0.86[EUR][1000 genomes]
rs1599381	0.89[EUR][1000 genomes]
rs1599383	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1599386	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599389	0.89[EUR][1000 genomes]
rs1599390	0.89[EUR][1000 genomes]
rs1609688	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1610158	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1993891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2306061	0.96[CEU][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2404340	0.80[ASN][1000 genomes]
rs2593812	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3849524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs4273380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4342141	0.92[CEU][hapmap]
rs4370045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs4414866	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4493449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4557202	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4597724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs4618258	0.89[CEU][hapmap]
rs4679924	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4679926	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5004752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6441354	0.96[CEU][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6441373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6762645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6765269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6765270	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6769642	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772578	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6774276	1.00[JPT][hapmap]
rs6774635	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[ASN][1000 genomes]
rs6778254	0.81[EUR][1000 genomes]
rs6783085	0.89[EUR][1000 genomes]
rs6789244	0.89[EUR][1000 genomes]
rs6789388	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6794601	0.89[TSI][hapmap]
rs6799130	0.88[EUR][1000 genomes]
rs6806054	0.89[CEU][hapmap]
rs7611367	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7614375	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7615592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7617204	0.89[EUR][1000 genomes]
rs7619011	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7622047	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs7625363	0.88[EUR][1000 genomes]
rs7628880	0.80[AMR][1000 genomes]
rs7629987	0.80[ASN][1000 genomes]
rs7630674	0.85[CEU][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630768	0.89[EUR][1000 genomes]
rs7632423	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs7632797	1.00[JPT][hapmap]
rs7633186	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs7633857	0.89[EUR][1000 genomes]
rs7637086	0.89[EUR][1000 genomes]
rs7647285	0.89[EUR][1000 genomes]
rs7647327	0.80[ASN][1000 genomes]
rs7650703	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651087	0.89[EUR][1000 genomes]
rs7653361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs778642	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs778643	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs778646	0.93[ASN][1000 genomes]
rs778649	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778653	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs778654	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs778657	0.89[CEU][hapmap]
rs778663	0.81[AMR][1000 genomes]
rs796609	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs898680	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898681	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9290065	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290069	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9290074	0.80[ASN][1000 genomes]
rs975323	0.80[ASN][1000 genomes]
rs980975	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs980976	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811594	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs9820825	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9821201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9831488	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs9846756	0.80[ASN][1000 genomes]
rs9847866	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848239	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860360	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9867582	0.86[EUR][1000 genomes]
rs9870059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9875200	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv963285	chr3:160848780-160856433	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4616689	PPM1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160844600-160859000	Weak transcription	Left Ventricle	heart
2	chr3:160850400-160882400	Weak transcription	Ovary	ovary
3	chr3:160855600-160861400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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