Variant report

Variant	rs12464255
Chromosome Location	chr2:208926542-208926543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:208393455..208396354-chr2:208925710..208928306,2	K562	blood:
2	chr2:208926371..208927250-chr2:208936763..208937685,3	MCF-7	breast:
3	chr2:208610533..208611358-chr2:208926502..208927536,4	MCF-7	breast:
4	chr2:208926513..208930859-chr2:208931530..208934190,4	K562	blood:
5	chr2:208489759..208491901-chr2:208925964..208928924,2	K562	blood:
6	chr2:208925382..208927634-chr2:208938153..208941077,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223725	Chromatin interaction
ENSG00000238582	Chromatin interaction
ENSG00000118260	Chromatin interaction
ENSG00000144401	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10192860	0.94[EUR][1000 genomes]
rs10497895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10932224	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12465052	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12465292	0.86[CEU][hapmap]
rs12470702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12471242	0.81[GIH][hapmap]
rs13428099	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13431014	0.86[CEU][hapmap]
rs16840403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17459758	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs17537670	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17538061	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17538138	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2362787	0.93[EUR][1000 genomes]
rs57709782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60335988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192772	0.91[EUR][1000 genomes]
rs62192773	0.91[EUR][1000 genomes]
rs62192790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192791	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62192812	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62192814	0.98[EUR][1000 genomes]
rs62192815	0.98[EUR][1000 genomes]
rs62192816	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62192818	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6435402	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs6740362	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]
rs72981543	0.95[EUR][1000 genomes]
rs72984907	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72984917	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72984926	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72984930	0.96[EUR][1000 genomes]
rs72984932	0.96[EUR][1000 genomes]
rs7588162	0.81[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap]
rs930745	0.81[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv875743	chr2:208688648-208940023	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12464255	DNMT3A	trans	cerebellum	SCAN
rs12464255	CREB1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:208912800-208929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:208926000-208927800	Enhancers	K562	blood
3	chr2:208926400-208928800	Enhancers	Fetal Brain Male	brain

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