Variant report

Variant	rs12418533
Chromosome Location	chr11:71955671-71955672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr11:71955341-71955811	SK-N-SH_RA	brain:	n/a	n/a
2	REST	chr11:71955040-71956347	SK-N-SH	brain:	n/a	chr11:71955614-71955627 chr11:71956125-71956138 chr11:71956121-71956141 chr11:71955462-71955469
3	YY1	chr11:71955454-71955805	SK-N-SH_RA	brain:	n/a	chr11:71955615-71955624
4	EP300	chr11:71955320-71955817	SK-N-SH_RA	brain:	n/a	n/a
5	SIN3A	chr11:71955153-71956543	H1-hESC	embryonic stem cell:	n/a	chr11:71955607-71955618
6	GTF2F1	chr11:71955662-71955800	H1-hESC	embryonic stem cell:	n/a	n/a
7	EGR1	chr11:71955407-71956108	H1-hESC	embryonic stem cell:	n/a	chr11:71955650-71955660 chr11:71955614-71955624 chr11:71955649-71955660 chr11:71955644-71955666 chr11:71955648-71955661
8	EGR1	chr11:71955534-71956018	H1-hESC	embryonic stem cell:	n/a	chr11:71955650-71955660 chr11:71955614-71955624 chr11:71955649-71955660 chr11:71955644-71955666 chr11:71955648-71955661
9	SP1	chr11:71955445-71955970	H1-hESC	embryonic stem cell:	n/a	chr11:71955614-71955624 chr11:71955665-71955679 chr11:71955614-71955623 chr11:71955613-71955625 chr11:71955615-71955624 chr11:71955613-71955625 chr11:71955614-71955624 chr11:71955614-71955623 chr11:71955614-71955628
10	RAD21	chr11:71955458-71955809	SK-N-SH_RA	brain:	n/a	chr11:71955617-71955627
11	ATF2	chr11:71955520-71955834	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr11:71953931-71956605	SK-N-SH	brain:	n/a	n/a
13	RAD21	chr11:71954948-71955881	SK-N-SH_RA	brain:	n/a	chr11:71955144-71955157 chr11:71955617-71955627
14	YY1	chr11:71955475-71955821	SK-N-SH_RA	brain:	n/a	chr11:71955615-71955624
15	JUND	chr11:71955568-71955787	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr11:71955336-71956137	H1-hESC	embryonic stem cell:	n/a	chr11:71955614-71955624 chr11:71955665-71955679 chr11:71955614-71955623 chr11:71955613-71955625 chr11:71955357-71955370 chr11:71955615-71955624 chr11:71955613-71955625 chr11:71955614-71955624 chr11:71955614-71955623 chr11:71955614-71955628
17	BACH1	chr11:71955407-71955757	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD1	chr11:71955500-71955673	H1-hESC	embryonic stem cell:	n/a	n/a
19	ZNF143	chr11:71955558-71956123	H1-hESC	embryonic stem cell:	n/a	n/a
20	EP300	chr11:71953915-71957050	SK-N-SH	brain:	n/a	chr11:71956843-71956856
21	GATA2	chr11:71955422-71955761	SH-SY5Y	brain:	n/a	n/a
22	CTBP2	chr11:71955388-71956913	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71951601..71953593-chr11:71954198..71956638,2	K562	blood:
2	chr11:71948375..71952014-chr11:71952052..71958381,8	MCF-7	breast:

Variant related genes	Relation type
PHOX2A	TF binding region
ENSG00000165462	Chromatin interaction
ENSG00000165458	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11548491	0.98[ASN][1000 genomes]
rs12416741	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs1783632	0.84[ASN][1000 genomes]
rs1784257	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs2276046	0.98[ASN][1000 genomes]
rs2508199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2508201	1.00[CHB][hapmap]
rs2508204	0.80[ASN][1000 genomes]
rs2508861	0.84[ASN][1000 genomes]
rs2508865	1.00[CHB][hapmap]
rs2508866	0.84[ASN][1000 genomes]
rs3900852	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs472837	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs477354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs487288	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs506041	0.84[ASN][1000 genomes]
rs527905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs55723921	0.84[ASN][1000 genomes]
rs56229279	0.84[ASN][1000 genomes]
rs56333926	0.84[ASN][1000 genomes]
rs58489620	0.84[ASN][1000 genomes]
rs590732	1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[MEX][hapmap];0.84[ASN][1000 genomes]
rs59427981	0.84[ASN][1000 genomes]
rs59509230	0.87[ASN][1000 genomes]
rs59980097	0.87[ASN][1000 genomes]
rs61736312	0.97[ASN][1000 genomes]
rs650834	0.82[ASN][1000 genomes]
rs70940824	0.94[ASN][1000 genomes]
rs7108974	0.84[ASN][1000 genomes]
rs7110260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs73528892	0.84[ASN][1000 genomes]
rs7952074	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs9886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv897908	chr11:71927468-71956890	ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897909	chr11:71927468-71960554	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3326211	chr11:71953829-71956677	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 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	chr11:71953000-71956000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr11:71954000-71956800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr11:71954200-71955800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr11:71954200-71956200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:71954400-71955800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr11:71954400-71955800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
7	chr11:71954400-71955800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr11:71954400-71955800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:71954400-71956800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr11:71954400-71957000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr11:71954600-71956400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:71954600-71956600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
13	chr11:71954600-71956800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr11:71954800-71955800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:71954800-71955800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
16	chr11:71954800-71956000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:71954800-71956000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:71954800-71956200	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:71954800-71956200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
20	chr11:71954800-71956400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr11:71954800-71956400	Enhancers	Lung	lung
22	chr11:71954800-71956600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:71954800-71956800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:71954800-71956800	Bivalent Enhancer	Fetal Brain Male	brain
25	chr11:71955000-71955800	Active TSS	Right Ventricle	heart
26	chr11:71955000-71956000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:71955200-71955800	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr11:71955200-71955800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
29	chr11:71955200-71955800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:71955200-71956200	Bivalent Enhancer	Fetal Thymus	thymus
31	chr11:71955200-71956600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr11:71955400-71955800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:71955400-71955800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr11:71955400-71955800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
35	chr11:71955400-71955800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr11:71955400-71955800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:71955400-71955800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
38	chr11:71955400-71955800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr11:71955400-71955800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
40	chr11:71955400-71955800	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr11:71955400-71955800	Bivalent Enhancer	Fetal Lung	lung
42	chr11:71955400-71955800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr11:71955400-71955800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr11:71955400-71956000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:71955400-71956000	Bivalent Enhancer	Brain Anterior Caudate	brain
46	chr11:71955400-71956000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr11:71955400-71956200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr11:71955400-71956200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:71955400-71956200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:71955400-71956200	Bivalent Enhancer	Brain Cingulate Gyrus	brain

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