Variant report

Variant	rs1542531
Chromosome Location	chr3:162256364-162256365
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:162248022..162250123-chr3:162255012..162257585,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1031837	0.85[ASN][1000 genomes]
rs10936294	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936295	0.90[ASN][1000 genomes]
rs12490335	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629492	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433947	0.85[ASN][1000 genomes]
rs13434303	0.88[ASN][1000 genomes]
rs1382200	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382201	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382202	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478140	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478141	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1478144	0.90[ASN][1000 genomes]
rs1478148	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1478149	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1478150	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1478151	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1531526	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531527	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531528	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1564172	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061734	0.90[ASN][1000 genomes]
rs2061736	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2061737	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2061738	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2061739	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2169726	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3863255	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885626	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3933788	0.90[ASN][1000 genomes]
rs3933789	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4856702	0.90[ASN][1000 genomes]
rs56239534	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58706084	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59229774	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441510	0.83[AMR][1000 genomes]
rs6441511	0.85[ASN][1000 genomes]
rs6441513	0.89[ASN][1000 genomes]
rs6441514	0.88[ASN][1000 genomes]
rs67118079	0.90[ASN][1000 genomes]
rs67203479	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67840917	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7428032	0.90[ASN][1000 genomes]
rs7428330	0.90[ASN][1000 genomes]
rs7429017	0.90[ASN][1000 genomes]
rs7431428	0.90[ASN][1000 genomes]
rs7433772	0.90[ASN][1000 genomes]
rs7433829	0.89[ASN][1000 genomes]
rs7613585	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7635791	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9283619	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813807	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9866048	0.88[ASN][1000 genomes]
rs9871703	0.89[ASN][1000 genomes]
rs993390	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs993393	0.83[AMR][1000 genomes]
rs997688	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877721	chr3:161878713-162303276	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877735	chr3:162123179-162380954	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv428424	chr3:162145988-163033943	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1012160	chr3:162182166-162540478	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1000912	chr3:162186601-162311128	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv592201	chr3:162188625-163142162	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv829775	chr3:162211618-162406402	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv470994	chr3:162217993-162945834	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv592205	chr3:162217994-162263832	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv877755	chr3:162218849-162386891	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv877756	chr3:162218849-162391801	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv877757	chr3:162226534-162391801	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1542531	IFT80	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162251800-162257400	Weak transcription	Dnd41	blood

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