Variant report

Variant	rs17619012
Chromosome Location	chr2:63893589-63893590
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	chr2:63885934..63888803-chr2:63891795..63894476,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10175674	0.89[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10496102	0.85[CEU][hapmap]
rs1109027	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12463603	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12470478	0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs12472865	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12988017	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap]
rs17618045	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2054120	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278718	0.85[CEU][hapmap]
rs36099158	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap]
rs3934536	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs4671070	0.83[ASN][1000 genomes]
rs4671072	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap]
rs4671535	1.00[CHB][hapmap]
rs6710230	0.82[JPT][hapmap]
rs72806010	0.80[EUR][1000 genomes]
rs72806056	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72806082	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72806087	0.91[ASN][1000 genomes]
rs72806089	0.82[AMR][1000 genomes];0.80[EUR][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	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv1792289	chr2:63812148-63900292	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
3	nsv834242	chr2:63891249-64045617	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17619012	CCT4	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63883600-63900400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:63888600-63893600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:63890600-63893800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:63891400-63895200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:63891800-63903400	Weak transcription	Aorta	Aorta
6	chr2:63892200-63894000	Enhancers	NHLF	lung
7	chr2:63892200-63895200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:63892400-63895600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:63892600-63895400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:63892600-63896200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:63892800-63893800	Enhancers	NH-A	brain
12	chr2:63892800-63895800	Enhancers	NHEK	skin
13	chr2:63893000-63893600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:63893000-63894000	Flanking Active TSS	NHDF-Ad	bronchial
15	chr2:63893000-63895600	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:63893000-63896400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:63893000-63896400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr2:63893000-63897800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:63893200-63893800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:63893200-63894000	Flanking Active TSS	Osteobl	bone
21	chr2:63893200-63895400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr2:63893200-63896400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:63893200-63898600	Enhancers	Adipose Nuclei	Adipose
24	chr2:63893400-63893600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:63893400-63893800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:63893400-63893800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:63893400-63893800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr2:63893400-63893800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:63893400-63894400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:63893400-63894400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:63893400-63895400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:63893400-63895400	Enhancers	HMEC	breast
33	chr2:63893400-63895600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:63893400-63895600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:63893400-63896200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr2:63893400-63896200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:63893400-63896400	Enhancers	Liver	Liver

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