Variant report

Variant	rs6802089
Chromosome Location	chr3:134544299-134544300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10935140	0.81[JPT][hapmap]
rs12489360	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap]
rs12630436	0.92[CEU][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs13068347	0.81[CHB][hapmap]
rs13073341	0.91[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs13078595	0.81[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs13078906	0.92[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1399706	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1515366	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs2280155	0.82[ASN][1000 genomes]
rs2280157	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs28434630	0.82[ASN][1000 genomes]
rs2895696	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs34201825	0.88[ASN][1000 genomes]
rs34226152	0.88[ASN][1000 genomes]
rs34898281	0.88[ASN][1000 genomes]
rs35223707	0.88[ASN][1000 genomes]
rs4955508	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs4955510	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6439530	0.81[CHB][hapmap]
rs6772947	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6782516	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs6786490	0.81[JPT][hapmap]
rs6789449	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793377	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs6796514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624092	0.80[ASN][1000 genomes]
rs7633880	0.81[ASN][1000 genomes]
rs7639520	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7639843	0.81[JPT][hapmap]
rs7643782	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs7645510	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645886	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.80[ASN][1000 genomes]
rs7645897	0.80[ASN][1000 genomes]
rs7646231	0.80[ASN][1000 genomes]
rs7653227	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs868130	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs884381	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs885594	0.87[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs938382	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs9814062	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814170	0.82[ASN][1000 genomes]
rs9814692	0.95[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9819889	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs9825632	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap]
rs9825687	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs9839573	0.81[JPT][hapmap]
rs9851596	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap]
rs9874291	0.81[JPT][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	nsv877515	chr3:134460368-134591138	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6802089	DZIP1L	cis	parietal	SCAN
rs6802089	UBA5	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134529600-134546400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:134534800-134546000	Weak transcription	Right Atrium	heart
3	chr3:134537800-134545600	Weak transcription	GM12878-XiMat	blood
4	chr3:134540600-134544600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr3:134541200-134547400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:134543000-134544400	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr3:134543400-134544400	Enhancers	Psoas Muscle	Psoas
8	chr3:134543600-134544400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:134543800-134546000	Weak transcription	Fetal Brain Male	brain
10	chr3:134544000-134546800	Weak transcription	Fetal Brain Female	brain

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