Variant report

Variant	rs1456009
Chromosome Location	chr2:46955185-46955186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46925799..46928213-chr2:46954632..46957949,3	MCF-7	breast:
2	chr2:46953820..46955350-chr2:46958244..46960079,2	K562	blood:
3	chr2:46924166..46927063-chr2:46954511..46956306,2	K562	blood:
4	chr2:46921430..46924294-chr2:46954187..46957185,2	MCF-7	breast:
5	chr2:46954874..46956811-chr2:46963158..46965367,2	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009230	1.00[CEU][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1009231	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167561	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10168342	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11125087	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12475080	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471056	0.95[ASN][1000 genomes]
rs1471057	0.85[ASN][1000 genomes]
rs1813505	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1867819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2045291	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061182	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738890	0.80[ASN][1000 genomes]
rs3768720	0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3814039	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4361172	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4522653	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4953414	0.82[ASN][1000 genomes]
rs4953415	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953418	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6544913	0.85[CHB][hapmap]
rs6544917	0.84[ASN][1000 genomes]
rs6544918	0.93[ASN][1000 genomes]
rs6544919	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6544921	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6705847	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6718658	0.83[YRI][hapmap]
rs6718677	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6721122	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6726345	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727737	0.83[CHB][hapmap];0.85[ASN][1000 genomes]
rs6727934	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6728559	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6728881	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6730949	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6740539	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs6741706	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6746471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6748938	0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7570376	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7580649	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897528	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs958726	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs991742	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46945400-46985400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:46947600-46975600	Weak transcription	HSMM	muscle
3	chr2:46948200-46955800	Weak transcription	Lung	lung
4	chr2:46948200-46956600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:46948200-46962000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:46948200-46964400	Weak transcription	NHEK	skin
7	chr2:46948200-46967400	Weak transcription	Esophagus	oesophagus
8	chr2:46948200-46974600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:46948200-46977200	Weak transcription	Aorta	Aorta
10	chr2:46948400-46961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:46948600-46964200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:46948600-46964400	Weak transcription	NH-A	brain
13	chr2:46948600-46974400	Weak transcription	Fetal Stomach	stomach
14	chr2:46948800-46955200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:46949600-46958400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:46950800-46958200	Weak transcription	NHLF	lung
17	chr2:46950800-46975400	Weak transcription	Fetal Lung	lung
18	chr2:46951400-46962200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:46951800-46959000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:46952000-46955200	Weak transcription	Primary B cells from cord blood	blood
21	chr2:46952000-46961800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:46952600-46955400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:46952600-46956400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:46952600-46962000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46952800-46957800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:46953000-46957800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:46953400-46955600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr2:46953400-46964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:46954200-46955200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:46954400-46955200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr2:46954400-46955200	Genic enhancers	HepG2	liver
32	chr2:46954400-46955400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:46954400-46955400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr2:46954400-46955400	Genic enhancers	A549	lung
35	chr2:46954400-46955600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr2:46954400-46955800	Genic enhancers	NHDF-Ad	bronchial
37	chr2:46954400-46957000	Genic enhancers	Osteobl	bone
38	chr2:46954600-46955200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:46954600-46955200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr2:46954600-46955200	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr2:46954600-46955200	Enhancers	Primary T cells from cord blood	blood
42	chr2:46954600-46955200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr2:46954600-46955200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr2:46954600-46955200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr2:46954600-46955200	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr2:46954600-46955200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr2:46954600-46955200	Enhancers	Thymus	Thymus
48	chr2:46954600-46955200	Enhancers	HUVEC	blood vessel
49	chr2:46954600-46955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:46954600-46955400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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