Variant report

Variant	rs6443582
Chromosome Location	chr3:178556483-178556484
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	chr3:178543542..178551305-chr3:178552157..178562303,11	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10804873	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs10936978	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11709071	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs11716970	0.82[ASN][1000 genomes]
rs11721205	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs11914342	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs11916314	0.82[ASN][1000 genomes]
rs11924270	0.83[ASN][1000 genomes]
rs11927078	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs11927700	0.82[ASN][1000 genomes]
rs11929676	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs13090876	0.82[ASN][1000 genomes]
rs28490096	0.82[ASN][1000 genomes]
rs28733874	0.82[ASN][1000 genomes]
rs3856779	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4131862	0.82[ASN][1000 genomes]
rs4131863	0.82[ASN][1000 genomes]
rs4258946	0.94[JPT][hapmap]
rs4414829	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4440105	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4498018	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4498019	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4542999	0.94[JPT][hapmap]
rs4549252	0.94[JPT][hapmap]
rs4624542	0.86[JPT][hapmap]
rs4624543	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs60725021	0.82[ASN][1000 genomes]
rs61798137	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6443581	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs6443583	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs6765556	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs6765682	0.85[ASN][1000 genomes]
rs6767499	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs6779867	0.82[ASN][1000 genomes]
rs6780023	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs6789905	0.85[ASN][1000 genomes]
rs6789945	1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[ASN][1000 genomes]
rs6796969	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804163	0.82[ASN][1000 genomes]
rs6809208	1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73053720	0.82[ASN][1000 genomes]
rs73053731	0.85[ASN][1000 genomes]
rs73053734	0.82[ASN][1000 genomes]
rs73053748	0.82[ASN][1000 genomes]
rs73882904	0.82[ASN][1000 genomes]
rs7618149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7640000	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs7642594	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs7643872	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs7646198	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9814677	0.82[ASN][1000 genomes]
rs9817052	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9817191	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9819352	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9819394	0.82[ASN][1000 genomes]
rs9819671	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9824836	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9828010	0.82[ASN][1000 genomes]
rs9828148	0.82[ASN][1000 genomes]
rs9828153	0.82[ASN][1000 genomes]
rs9831934	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9833798	0.85[ASN][1000 genomes]
rs9837702	0.82[ASN][1000 genomes]
rs9844536	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9844737	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs9851600	0.84[ASN][1000 genomes]
rs9853141	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9853436	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9855019	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs9857760	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18827	chr3:178550206-178568168	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
2	nsv592645	chr3:178550246-178568129	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv592646	chr3:178555598-178566442	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6443582	CBFA2T2	trans	cerebellum	SCAN
rs6443582	ABCF3	cis	parietal	SCAN
rs6443582	TTC14	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178541200-178558400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:178542000-178563600	Weak transcription	Aorta	Aorta
3	chr3:178545200-178557800	Weak transcription	Fetal Muscle Leg	muscle
4	chr3:178546400-178563000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:178550400-178562800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:178556200-178558400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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