Variant report

Variant	rs754298
Chromosome Location	chr3:50548895-50548896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50357043..50359175-chr3:50546790..50549630,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068001	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11130255	0.81[CEU][hapmap]
rs11719998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12491425	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12493985	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs129310	0.81[EUR][1000 genomes]
rs13094785	0.82[CEU][hapmap]
rs13096264	0.82[CEU][hapmap]
rs1458387	0.82[CEU][hapmap]
rs2125369	0.80[CEU][hapmap]
rs2168866	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs2232248	0.81[CHD][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs2269505	0.81[CHD][hapmap];0.82[MEX][hapmap]
rs2355323	0.82[EUR][1000 genomes]
rs2609036	0.82[CEU][hapmap]
rs375544	0.81[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs3792325	0.87[CEU][hapmap]
rs3792328	0.82[CEU][hapmap];0.93[TSI][hapmap]
rs3804627	0.81[CHD][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs3804628	0.82[CEU][hapmap]
rs391620	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3943212	0.82[CEU][hapmap]
rs396302	0.82[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs398703	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs399971	0.80[EUR][1000 genomes]
rs414171	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs417592	0.81[CHD][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs441516	0.82[EUR][1000 genomes]
rs443030	0.81[EUR][1000 genomes]
rs443436	0.82[CEU][hapmap]
rs448028	0.82[CEU][hapmap]
rs453570	0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs4688712	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs616589	0.87[CEU][hapmap]
rs628081	0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446212	0.82[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6776224	0.80[CEU][hapmap]
rs6778680	0.87[CEU][hapmap]
rs6779819	0.82[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs6791880	0.82[CEU][hapmap];0.93[TSI][hapmap]
rs6796769	0.82[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs695170	0.82[EUR][1000 genomes]
rs728901	0.82[CEU][hapmap]
rs750453	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs750510	0.84[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7611428	0.82[CEU][hapmap];0.86[TSI][hapmap]
rs7615703	0.82[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs7646236	0.81[CHD][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs809451	0.82[CEU][hapmap]
rs809454	0.82[JPT][hapmap]
rs813243	0.82[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs900735	0.82[CEU][hapmap]
rs9682401	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs754298	MST1	cis	cerebellum	SCAN
rs754298	ALS2CL	cis	parietal	SCAN
rs754298	CAMP	cis	cerebellum	SCAN
rs754298	NBEAL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50541600-50552200	Weak transcription	Spleen	Spleen
2	chr3:50547600-50549600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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