Variant report

Variant	rs329489
Chromosome Location	chr2:64263530-64263531
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	chr2:64256991..64258692-chr2:64262523..64264445,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10168446	0.88[ASN][1000 genomes]
rs10199273	0.85[ASN][1000 genomes]
rs11125987	0.85[ASN][1000 genomes]
rs11682249	0.81[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11692514	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12464534	0.82[ASN][1000 genomes]
rs12988868	0.81[ASN][1000 genomes]
rs12991346	0.93[ASN][1000 genomes]
rs13014371	0.92[ASN][1000 genomes]
rs13021953	0.91[ASN][1000 genomes]
rs13023231	0.90[ASN][1000 genomes]
rs13034625	0.92[ASN][1000 genomes]
rs1421093	0.90[ASN][1000 genomes]
rs1440003	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs193031	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs2164735	0.81[EUR][1000 genomes]
rs329479	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329480	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs329486	0.85[CHB][hapmap]
rs329487	0.84[ASN][1000 genomes]
rs329488	0.91[AFR][1000 genomes]
rs329490	0.83[ASN][1000 genomes]
rs34506208	0.91[ASN][1000 genomes]
rs34688719	0.89[ASN][1000 genomes]
rs4616468	0.81[ASN][1000 genomes]
rs6546031	0.80[ASN][1000 genomes]
rs6546041	0.90[ASN][1000 genomes]
rs67247064	0.89[ASN][1000 genomes]
rs6755041	0.82[ASN][1000 genomes]
rs6758381	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs329489	CCT4	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64251200-64273200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:64261200-64266200	Weak transcription	HepG2	liver
3	chr2:64261400-64263800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:64261800-64263800	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr2:64261800-64264200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:64261800-64264800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr2:64262000-64263600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr2:64262200-64263600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:64262200-64263600	Enhancers	Thymus	Thymus
10	chr2:64262200-64263800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:64262200-64263800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:64262200-64264400	Enhancers	Primary T cells fromperipheralblood	blood
13	chr2:64262400-64263600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:64262400-64263600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:64262400-64263800	Enhancers	HSMM	muscle
16	chr2:64262400-64264000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:64262600-64263800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:64262600-64264000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:64262800-64263600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:64262800-64263800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:64262800-64264000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:64262800-64264000	Enhancers	NHEK	skin
23	chr2:64262800-64264400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:64263000-64263600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:64263000-64263600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:64263000-64263800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:64263000-64264000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:64263000-64264000	Enhancers	NHDF-Ad	bronchial
29	chr2:64263200-64263600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:64263200-64263600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:64263200-64263600	Enhancers	Primary hematopoietic stem cells	blood
32	chr2:64263200-64263600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:64263200-64263600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr2:64263200-64263600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:64263200-64263600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr2:64263200-64263600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:64263200-64263600	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr2:64263200-64263600	Flanking Active TSS	Dnd41	blood
39	chr2:64263200-64263600	Flanking Active TSS	GM12878-XiMat	blood
40	chr2:64263200-64263600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:64263200-64263600	Flanking Active TSS	Osteobl	bone
42	chr2:64263200-64263800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:64263200-64263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:64263200-64263800	Enhancers	Fetal Thymus	thymus
45	chr2:64263200-64263800	Enhancers	HMEC	breast
46	chr2:64263200-64263800	Enhancers	NHLF	lung
47	chr2:64263200-64264000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:64263200-64264000	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr2:64263200-64264000	Enhancers	Primary B cells from peripheral blood	blood
50	chr2:64263200-64264000	Enhancers	HUVEC	blood vessel

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