Variant report

Variant	rs6829402
Chromosome Location	chr4:76503197-76503198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11097070	0.89[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs11736474	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11737705	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13116639	0.82[EUR][1000 genomes]
rs13118426	0.82[EUR][1000 genomes]
rs13133699	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13137468	0.82[EUR][1000 genomes]
rs13138717	0.82[EUR][1000 genomes]
rs13140908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1464070	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1464071	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546539	0.82[EUR][1000 genomes]
rs1548175	0.82[EUR][1000 genomes]
rs1553984	1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1553986	0.82[EUR][1000 genomes]
rs1967495	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs1967496	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs3796473	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3796485	0.82[EUR][1000 genomes]
rs3796488	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3853183	0.90[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs4337757	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4349625	0.82[EUR][1000 genomes]
rs4859403	0.82[EUR][1000 genomes]
rs4859537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4859542	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4859543	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs4859546	0.82[EUR][1000 genomes]
rs4859547	0.91[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs4859548	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs6531778	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531841	0.82[EUR][1000 genomes]
rs6531866	0.82[EUR][1000 genomes]
rs6531867	0.81[EUR][1000 genomes]
rs6531868	0.81[EUR][1000 genomes]
rs6826858	0.83[ASW][hapmap];0.90[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap]
rs6827809	0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs6832912	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6835702	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7659408	0.82[EUR][1000 genomes]
rs7672378	0.82[EUR][1000 genomes]
rs7674328	1.00[ASW][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7685459	0.80[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7691765	0.82[EUR][1000 genomes]

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	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6829402	PPEF2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76499200-76506200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:76499200-76509200	Weak transcription	Stomach Smooth Muscle	stomach

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