Variant report

Variant	rs572046
Chromosome Location	chr12:65055535-65055536
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65052809..65057166-chr12:65058772..65061911,4	MCF-7	breast:
2	chr12:65054561..65056849-chr12:65066939..65068570,2	K562	blood:
3	chr12:65054544..65056091-chr12:65072277..65074215,2	MCF-7	breast:
4	chr12:65003105..65006170-chr12:65055260..65058498,3	MCF-7	breast:
5	chr12:65054936..65056811-chr12:65063750..65065750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256670	Chromatin interaction
ENSG00000153179	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10748011	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175496	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147097	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1147104	0.91[EUR][1000 genomes]
rs1147106	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1244870	0.82[ASN][1000 genomes]
rs1244871	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1244872	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1244881	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1245170	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1261879	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264239	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1270430	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1690261	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1716497	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1716518	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795614	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1795617	0.87[EUR][1000 genomes]
rs1797690	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1797699	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682713	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682717	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2682721	0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264239	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577303	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307999	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308397	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[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	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65025000-65059600	Weak transcription	Thymus	Thymus
2	chr12:65028600-65056400	Weak transcription	NHEK	skin
3	chr12:65033600-65059400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:65043600-65059600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:65044000-65059400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:65045800-65056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:65046400-65058600	Weak transcription	Ovary	ovary
8	chr12:65047000-65056400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:65047000-65059400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:65047200-65059400	Weak transcription	Fetal Stomach	stomach
11	chr12:65047400-65059400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:65047800-65056000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:65047800-65056400	Weak transcription	Hela-S3	cervix
14	chr12:65047800-65056600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:65047800-65059400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:65047800-65059400	Weak transcription	NHLF	lung
17	chr12:65047800-65063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:65048000-65060400	Weak transcription	Dnd41	blood
19	chr12:65048000-65063000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:65048400-65062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:65048600-65059400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:65048800-65060200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:65049000-65059600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr12:65049200-65058800	Weak transcription	K562	blood
25	chr12:65049200-65062200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:65049400-65055800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:65049400-65059000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:65049800-65059600	Weak transcription	Placenta	Placenta
29	chr12:65050400-65059400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:65050400-65059400	Weak transcription	NH-A	brain
31	chr12:65050600-65058800	Weak transcription	Liver	Liver
32	chr12:65051400-65057000	Enhancers	Fetal Heart	heart
33	chr12:65051600-65056400	Weak transcription	HMEC	breast
34	chr12:65051600-65056600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:65051600-65060600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:65051800-65056800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:65051800-65056800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:65052200-65057200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr12:65052600-65056200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:65052800-65059200	Weak transcription	Lung	lung
41	chr12:65052800-65059400	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:65053000-65056400	Weak transcription	Gastric	stomach
43	chr12:65053000-65057200	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr12:65053000-65058400	Weak transcription	Primary B cells from cord blood	blood
45	chr12:65053000-65058800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:65053000-65059400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:65053000-65059400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr12:65053000-65059600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:65053200-65055800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:65053200-65056400	Weak transcription	Fetal Lung	lung

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