Variant report

Variant	rs9534965
Chromosome Location	chr13:48709605-48709606
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48707167..48708993-chr13:48709200..48711032,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224510	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11616639	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1410117	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1571256	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.81[ASN][1000 genomes]
rs1927213	0.81[ASN][1000 genomes]
rs2104480	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs2148246	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2148938	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2406709	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2406797	0.81[ASN][1000 genomes]
rs4294712	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4369555	0.88[CEU][hapmap];0.90[JPT][hapmap]
rs4941623	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4942748	0.81[ASN][1000 genomes]
rs55633570	0.86[AMR][1000 genomes]
rs56399021	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61973324	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7324484	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs7326363	0.82[ASN][1000 genomes]
rs7336214	0.81[ASN][1000 genomes]
rs8001243	0.80[ASN][1000 genomes]
rs9526442	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9526443	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9526445	0.81[ASN][1000 genomes]
rs9526447	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526449	0.83[ASN][1000 genomes]
rs9534888	0.88[CEU][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs9534895	0.82[AMR][1000 genomes]
rs9534900	0.86[AMR][1000 genomes]
rs9534931	0.92[AMR][1000 genomes]
rs9534933	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9534937	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9534939	0.96[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9534944	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9534946	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9534947	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9534948	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9534950	0.81[ASN][1000 genomes]
rs9534951	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9534952	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9534957	0.82[ASN][1000 genomes]
rs9534961	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9567994	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs9568014	0.86[CHB][hapmap];0.86[JPT][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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9534965	SUCLA2	cis	parietal	SCAN
rs9534965	ENOX1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48701800-48725800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:48702200-48713800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:48706000-48710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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