Variant report

Variant	rs2754530
Chromosome Location	chr2:31803403-31803404
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	chr17:79477743..79480013-chr2:31802831..31804797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184009	Chromatin interaction
ENSG00000266077	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10207755	0.87[ASN][1000 genomes]
rs12467911	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2208532	0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2268796	0.80[MEX][hapmap]
rs2268799	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300697	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2300698	0.84[ASN][1000 genomes]
rs2300699	0.82[ASN][1000 genomes]
rs2300701	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4952197	0.82[CHB][hapmap]
rs499362	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502139	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs522638	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs523349	0.87[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs524345	0.89[ASN][1000 genomes]
rs527112	0.85[ASN][1000 genomes]
rs553464	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs559555	0.90[ASN][1000 genomes]
rs569320	0.81[ASN][1000 genomes]
rs589427	0.83[ASN][1000 genomes]
rs599300	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs607294	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs608574	0.87[ASN][1000 genomes]
rs623419	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs632148	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6749019	0.87[ASN][1000 genomes]
rs676033	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs681482	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs682895	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs725631	0.81[ASN][1000 genomes]
rs765138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs806645	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv456030	chr2:31598823-31820256	Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv456041	chr2:31598823-31820256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv581269	chr2:31598823-31820256	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv998853	chr2:31601455-31858961	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005565	chr2:31603134-31868877	Genic enhancers Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1007179	chr2:31616112-31835410	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1005032	chr2:31616112-31867450	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1013891	chr2:31629179-31854283	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv535612	chr2:31629179-31854283	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1002988	chr2:31767131-31996924	Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2754530	SLC30A6	cis	parietal	SCAN
rs2754530	NLRC4	cis	parietal	SCAN
rs2754530	SLC30A6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31803000-31803800	Weak transcription	Liver	Liver
2	chr2:31803400-31804000	Enhancers	HepG2	liver

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