Variant report

Variant	rs269402
Chromosome Location	chr1:67341984-67341985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1104705	0.82[CEU][hapmap]
rs11208967	0.82[CEU][hapmap]
rs11208968	0.82[CEU][hapmap]
rs12023158	0.82[CEU][hapmap]
rs12045569	0.82[CEU][hapmap]
rs12239035	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239074	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1280338	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1925399	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925400	0.94[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925401	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925402	0.85[ASW][hapmap];0.87[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1925403	0.94[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1925404	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925405	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1925406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1931297	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2147835	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2147836	0.88[CEU][hapmap]
rs269395	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs269399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs269401	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs269403	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs269405	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991353	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991354	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2991359	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255358	0.82[EUR][1000 genomes]
rs4655653	0.82[CEU][hapmap]
rs496070	0.88[CEU][hapmap]
rs55858354	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56400880	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs573490	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs576078	0.82[CEU][hapmap];0.80[LWK][hapmap];0.90[MKK][hapmap]
rs61467716	0.87[EUR][1000 genomes]
rs6699606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671671	0.82[EUR][1000 genomes]
rs72671673	0.83[EUR][1000 genomes]
rs72671674	0.80[EUR][1000 genomes]
rs72671675	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671677	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671679	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671680	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72671682	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72671685	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7552770	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869413	chr1:67082512-67414286	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv830093	chr1:67173594-67348264	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv546443	chr1:67268642-67352960	Genic enhancers Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871738	chr1:67268642-67375206	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv871259	chr1:67275027-67375206	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs269402	MIER1	cis	parietal	SCAN
rs269402	GADD45A	cis	cerebellum	SCAN
rs269402	WDR78	cis	parietal	SCAN
rs269402	WLS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67336200-67344000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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