Variant report

Variant	rs17340282
Chromosome Location	chr3:100764818-100764819
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	chr3:100759370..100761193-chr3:100762880..100765226,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13085823	0.89[ASN][1000 genomes]
rs1375512	0.89[ASN][1000 genomes]
rs1449299	0.81[ASN][1000 genomes]
rs1579969	0.89[ASN][1000 genomes]
rs16843153	0.89[ASN][1000 genomes]
rs16843185	0.89[ASN][1000 genomes]
rs17339226	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs1836985	0.86[CHB][hapmap]
rs2595907	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.92[MEX][hapmap]
rs2713749	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.92[MEX][hapmap];0.81[ASN][1000 genomes]
rs2713758	0.85[ASN][1000 genomes]
rs2713798	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap]
rs55687619	0.81[ASN][1000 genomes]
rs56077494	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56237429	0.81[ASN][1000 genomes]
rs59476872	0.89[ASN][1000 genomes]
rs6774218	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6787197	0.89[ASN][1000 genomes]
rs6787878	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73141447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73143061	0.81[ASN][1000 genomes]
rs73143062	0.81[ASN][1000 genomes]
rs73143064	0.81[ASN][1000 genomes]
rs73143072	0.81[ASN][1000 genomes]
rs73144908	0.81[ASN][1000 genomes]
rs73144910	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73144915	0.81[ASN][1000 genomes]
rs73144970	0.89[ASN][1000 genomes]
rs73149160	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73149173	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621518	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7623956	0.84[CEU][hapmap];0.81[ASN][1000 genomes]
rs7625454	0.85[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7641631	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.81[ASN][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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv591176	chr3:100763611-100799644	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17340282	ABI3BP	cis	parietal	SCAN
rs17340282	CEP97	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100762600-100780200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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