Variant report

Variant	rs7309234
Chromosome Location	chr12:39928435-39928436
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	chr12:39836470..39838324-chr12:39927543..39930505,2	MCF-7	breast:
2	chr12:39926553..39928856-chr12:39931123..39933872,2	K562	blood:

Variant related genes	Relation type
ENSG00000270273	Chromatin interaction
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10877173	0.92[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172144	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs11172162	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs11172366	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172480	0.92[ASN][1000 genomes]
rs11172488	0.83[ASN][1000 genomes]
rs11172616	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172645	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172646	0.86[ASN][1000 genomes]
rs11172647	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172687	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172692	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172697	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172713	0.80[JPT][hapmap]
rs11172722	0.80[JPT][hapmap]
rs11172794	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11172848	0.92[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs11172896	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11172897	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12227286	0.92[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12227668	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12228013	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes]
rs12228617	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12229160	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12229370	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12230055	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1512941	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs17127070	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs17127094	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs17127129	1.00[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17127138	0.93[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2292491	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs35790935	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35858791	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072006	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4285917	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4294600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4298947	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4639970	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57847223	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58036566	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59518553	0.86[ASN][1000 genomes]
rs59528535	0.86[ASN][1000 genomes]
rs61258856	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6581228	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7133376	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7133599	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7294474	0.97[EUR][1000 genomes]
rs7302302	0.97[EUR][1000 genomes]
rs7308138	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs73088816	0.97[EUR][1000 genomes]
rs73094447	0.97[EUR][1000 genomes]
rs73094449	0.97[EUR][1000 genomes]
rs73094488	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310178	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7310871	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7312611	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs73268358	0.86[ASN][1000 genomes]
rs73268359	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs74086536	0.97[EUR][1000 genomes]
rs7966841	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7970944	0.97[EUR][1000 genomes]
rs7976275	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs7980595	1.00[CEU][hapmap];0.90[JPT][hapmap]

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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1048933	chr12:39886665-39946270	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1039645	chr12:39903123-40022029	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7309234	ABCD2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39926000-39934600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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