Variant report

Variant	rs2269939
Chromosome Location	chr12:120242262-120242263
allele	C/T
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	FOSL2	chr12:120242039-120242536	MCF-7	breast:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
2	CTCF	chr12:120242164-120242470	MCF-7	breast:	n/a	n/a
3	CTCF	chr12:120242200-120242350	AG04450	lung:	n/a	n/a
4	MAX	chr12:120242232-120242379	NB4	blood:	n/a	chr12:120242306-120242315
5	TCF12	chr12:120242152-120242364	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr12:120242198-120242449	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr12:120242238-120242425	HepG2	liver:	n/a	n/a
8	FOSL1	chr12:120242152-120242476	K562	blood:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316 chr12:120242305-120242316
9	E2F6	chr12:120241999-120242484	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr12:120242240-120242390	NHLF	lung:	n/a	n/a
11	JUND	chr12:120242168-120242593	Hela-S3	cervix:	n/a	chr12:120242305-120242316 chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
12	POLR2A	chr12:120241995-120242546	H1-neurons	neurons:	n/a	n/a
13	GTF2F1	chr12:120242194-120242430	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr12:120242155-120242466	MCF-7	breast:	n/a	n/a
15	CTCF	chr12:120242150-120242494	MCF-7	breast:	n/a	n/a
16	RAD21	chr12:120242204-120242552	SK-N-SH_RA	brain:	n/a	n/a
17	CTCF	chr12:120242260-120242410	HMF	breast:	n/a	n/a
18	MYC	chr12:120242138-120242431	MCF-7	breast:	n/a	chr12:120242306-120242315
19	FOXA1	chr12:120242164-120242471	T-47D	breast:	n/a	n/a
20	SIN3AK20	chr12:120242141-120242397	K562	blood:	n/a	n/a
21	MAX	chr12:120242034-120242490	ECC-1	luminal epithelium:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
22	CTCF	chr12:120242160-120242310	GM12864	blood:	n/a	n/a
23	CTCF	chr12:120242182-120242562	A549	lung:	n/a	n/a
24	POLR2A	chr12:120242165-120242312	H1-hESC	embryonic stem cell:	n/a	n/a
25	EP300	chr12:120242114-120242515	SK-N-SH_RA	brain:	n/a	n/a
26	CTCF	chr12:120242240-120242390	HA-sp	spinal cord:	n/a	n/a
27	JUND	chr12:120242109-120242479	H1-hESC	embryonic stem cell:	n/a	chr12:120242305-120242316 chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
28	CTCF	chr12:120242200-120242350	A549	lung:	n/a	n/a
29	CTCF	chr12:120242179-120242460	MCF-7	breast:	n/a	n/a
30	ATF3	chr12:120242187-120242519	K562	blood:	n/a	n/a
31	CTCF	chr12:120242153-120242506	K562	blood:	n/a	n/a
32	CTCF	chr12:120241693-120242868	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr12:120242240-120242390	GM12875	blood:	n/a	n/a
34	CEBPB	chr12:120242184-120242384	H1-hESC	embryonic stem cell:	n/a	n/a
35	MXI1	chr12:120241760-120242613	IMR90	lung:	n/a	n/a
36	MYC	chr12:120242159-120242426	H1-hESC	embryonic stem cell:	n/a	chr12:120242306-120242315
37	CTCF	chr12:120242137-120242467	Fibrobl	skin:	n/a	n/a
38	HMGN3	chr12:120242091-120242412	K562	blood:	n/a	n/a
39	FOS	chr12:120242108-120242503	MCF10A-Er-Src	breast:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242305-120242316 chr12:120242307-120242316
40	CTCF	chr12:120242175-120242475	HepG2	liver:	n/a	n/a
41	FOSL2	chr12:120242159-120242476	A549	lung:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
42	JUND	chr12:120242133-120242515	HepG2	liver:	n/a	chr12:120242305-120242316 chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
43	CREB1	chr12:120242104-120242500	A549	lung:	n/a	n/a
44	MYC	chr12:120242120-120242314	MCF-7	breast:	n/a	chr12:120242124-120242133
45	CTCF	chr12:120242193-120242424	LNCaP	prostate:	n/a	n/a
46	CHD2	chr12:120241997-120242489	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr12:120242200-120242350	NB4	blood:	n/a	n/a
48	CTCF	chr12:120242236-120242454	Medullo	brain:	n/a	n/a
49	CTCF	chr12:120242242-120242431	GM13977	blood:	n/a	n/a
50	CTCF	chr12:120242174-120242458	NHEK	skin:	n/a	n/a

Variant related genes	Relation type
CIT	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10774517	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10774519	0.82[ASW][hapmap];0.88[YRI][hapmap]
rs11064908	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11609520	0.89[CEU][hapmap];0.87[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11615808	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11615832	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs203339	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs203342	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203343	0.89[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs203352	0.87[CHB][hapmap]
rs2269938	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs278109	0.82[ASW][hapmap]
rs278128	0.82[ASW][hapmap]
rs278130	0.82[ASW][hapmap]
rs3847958	0.84[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4766951	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs6490271	0.95[CEU][hapmap];0.87[CHB][hapmap];0.97[EUR][1000 genomes]
rs7309586	0.84[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7954961	0.82[ASW][hapmap];0.81[GIH][hapmap]
rs7979697	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120190000-120244800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:120209400-120293600	Weak transcription	Primary T cells from cord blood	blood
3	chr12:120223000-120255800	Weak transcription	HepG2	liver
4	chr12:120223000-120314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:120229000-120242400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:120229400-120256600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:120231000-120244800	Strong transcription	Dnd41	blood
8	chr12:120231200-120243800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:120232000-120246000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:120235000-120243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:120235800-120244600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:120237200-120246400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:120237400-120250600	Weak transcription	Hela-S3	cervix
14	chr12:120238000-120242400	Active TSS	Brain Angular Gyrus	brain
15	chr12:120238000-120242400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr12:120239200-120242400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:120239400-120242400	Active TSS	Brain Hippocampus Middle	brain
18	chr12:120239800-120242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:120239800-120242600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:120240400-120242400	Active TSS	Fetal Brain Female	brain
21	chr12:120240400-120242800	Strong transcription	Fetal Thymus	thymus
22	chr12:120240400-120244600	Weak transcription	GM12878-XiMat	blood
23	chr12:120240600-120242800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr12:120241000-120242400	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:120241000-120242400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:120241000-120242400	Active TSS	Fetal Kidney	kidney
27	chr12:120241000-120242400	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr12:120241000-120242400	ZNF genes & repeats	Thymus	Thymus
29	chr12:120241000-120242600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:120241000-120242600	Active TSS	Fetal Intestine Large	intestine
31	chr12:120241000-120242600	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr12:120241000-120242800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:120241200-120242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:120241200-120242600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr12:120241200-120242600	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:120241200-120242800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:120241400-120242400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:120241400-120242600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:120241400-120242600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr12:120241400-120242600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:120241400-120242600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr12:120241400-120242600	Flanking Active TSS	Fetal Stomach	stomach
43	chr12:120241400-120242600	Flanking Active TSS	NH-A	brain
44	chr12:120241400-120242800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr12:120241400-120242800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:120241400-120242800	Flanking Active TSS	Osteobl	bone
47	chr12:120241600-120242600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:120241600-120242600	Enhancers	Right Ventricle	heart
49	chr12:120241600-120242800	Flanking Active TSS	NHDF-Ad	bronchial
50	chr12:120241600-120242800	Flanking Active TSS	NHLF	lung

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