Variant report

Variant	rs13072228
Chromosome Location	chr3:59964546-59964547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11707783	0.81[CHD][hapmap]
rs11711589	0.82[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11921436	0.82[ASN][1000 genomes]
rs13064036	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13075410	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13077692	0.86[YRI][hapmap];0.87[AFR][1000 genomes]
rs1879996	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs212034	0.95[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2630189	0.83[ASN][1000 genomes]
rs2736794	0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2736796	0.84[ASN][1000 genomes]
rs2736802	0.95[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs3772475	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3772476	0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.88[ASN][1000 genomes]
rs3772477	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3772480	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772482	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772484	0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6446100	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6446101	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6446102	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6446103	0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6446104	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6771698	0.84[EUR][1000 genomes]
rs6805337	0.84[EUR][1000 genomes]
rs7626003	0.92[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs802775	0.82[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9819930	0.82[CHD][hapmap]
rs9865672	0.82[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9880771	0.81[ASN][1000 genomes]
rs9881070	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13072228	CCDC66	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59961600-59969000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:59962000-59964600	Weak transcription	Dnd41	blood
3	chr3:59962800-59964600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:59963000-59969400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr3:59963800-59964800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:59964000-59967800	Enhancers	Primary T cells from cord blood	blood
7	chr3:59964200-59967400	Enhancers	Fetal Thymus	thymus
8	chr3:59964400-59964600	Enhancers	GM12878-XiMat	blood
9	chr3:59964400-59965000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:59964400-59967400	Enhancers	Thymus	Thymus
11	chr3:59964400-59968400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:59964400-59970600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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