Variant report

Variant	rs2269938
Chromosome Location	chr12:120242014-120242015
allele	C/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	E2F6	chr12:120241999-120242484	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:120241995-120242546	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr12:120241900-120242050	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr12:120241882-120242051	Fibrobl	skin:	n/a	n/a
5	CTCF	chr12:120241920-120242070	AG09319	gingival:	n/a	n/a
6	CTCF	chr12:120241693-120242868	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr12:120241760-120242613	IMR90	lung:	n/a	n/a
8	CTCF	chr12:120241900-120242050	AoAF	blood vessel:	n/a	n/a
9	CHD2	chr12:120241997-120242489	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr12:120241880-120242030	HAc	cerebellar:	n/a	n/a
11	JUND	chr12:120241902-120242516	H1-hESC	embryonic stem cell:	n/a	chr12:120242305-120242316 chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
12	CTCF	chr12:120241880-120242030	BJ	skin:	n/a	n/a
13	MAX	chr12:120242011-120242466	SK-N-SH	brain:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
14	E2F6	chr12:120241860-120242525	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr12:120241880-120242030	HMF	breast:	n/a	n/a
16	CTCF	chr12:120241880-120242030	AG09309	skin:	n/a	n/a
17	POLR2A	chr12:120241972-120242610	H1-neurons	neurons:	n/a	n/a
18	YY1	chr12:120241872-120242518	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr12:120240141-120242788	H1-neurons	neurons:	n/a	chr12:120242040-120242053
20	MYC	chr12:120241928-120242417	MCF-7	breast:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
21	FOSL2	chr12:120242006-120242649	SK-N-SH	brain:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
22	CTCF	chr12:120241900-120242050	HPAF	blood vessel:	n/a	n/a
23	MAX	chr12:120241995-120242541	A549	lung:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
24	MAX	chr12:120242008-120242563	MCF-7	breast:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
25	CTCF	chr12:120241900-120242050	NHDF-neo	bronchial:	n/a	n/a
26	MAX	chr12:120241972-120242527	H1-hESC	embryonic stem cell:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
27	CTCF	chr12:120241920-120242070	HMEC	breast:	n/a	n/a
28	JUN	chr12:120242001-120242531	K562	blood:	n/a	chr12:120242303-120242314 chr12:120242306-120242317 chr12:120242305-120242312 chr12:120242307-120242316
29	MXI1	chr12:120241035-120243037	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr12:120241874-120242169	MCF-7	breast:	n/a	n/a
31	SIN3A	chr12:120241791-120242578	H1-hESC	embryonic stem cell:	n/a	chr12:120241985-120241996
32	SIN3AK20	chr12:120241914-120242495	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:120241880-120242030	AG10803	skin:	n/a	n/a
34	POLR2A	chr12:120241873-120242277	MCF-7	breast:	n/a	n/a
35	ZKSCAN1	chr12:120241899-120242405	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr12:120241920-120242070	BJ	skin:	n/a	n/a
37	POLR2A	chr12:120241859-120242040	H1-hESC	embryonic stem cell:	n/a	n/a
38	CREB1	chr12:120241957-120242598	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr12:120241965-120242764	SK-N-SH	brain:	n/a	chr12:120242070-120242083
40	MAX	chr12:120241975-120242552	H1-hESC	embryonic stem cell:	n/a	chr12:120242306-120242315 chr12:120242124-120242133
41	CTCF	chr12:120241880-120242030	AG04449	skin:	n/a	n/a

Variant related genes	Relation type
CIT	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10774518	1.00[JPT][hapmap]
rs10774519	0.95[JPT][hapmap]
rs11609520	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615808	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11615832	0.94[EUR][1000 genomes]
rs203339	0.95[CEU][hapmap]
rs203342	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs203343	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs203352	0.96[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2269939	0.95[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3847958	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490271	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7309586	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs7954961	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs7979697	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes]

No data

Chromatin state (count:105 , 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	chr12:120239200-120242200	Active TSS	Brain Substantia Nigra	brain
17	chr12:120239200-120242400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:120239400-120242400	Active TSS	Brain Hippocampus Middle	brain
19	chr12:120239800-120242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:120239800-120242600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:120240400-120242400	Active TSS	Fetal Brain Female	brain
22	chr12:120240400-120242800	Strong transcription	Fetal Thymus	thymus
23	chr12:120240400-120244600	Weak transcription	GM12878-XiMat	blood
24	chr12:120240600-120242800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr12:120241000-120242200	Flanking Active TSS	Fetal Brain Male	brain
26	chr12:120241000-120242200	Active TSS	Fetal Intestine Small	intestine
27	chr12:120241000-120242200	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:120241000-120242200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr12:120241000-120242400	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr12:120241000-120242400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:120241000-120242400	Active TSS	Fetal Kidney	kidney
32	chr12:120241000-120242400	Flanking Active TSS	Fetal Muscle Trunk	muscle
33	chr12:120241000-120242400	ZNF genes & repeats	Thymus	Thymus
34	chr12:120241000-120242600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:120241000-120242600	Active TSS	Fetal Intestine Large	intestine
36	chr12:120241000-120242600	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr12:120241000-120242800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:120241200-120242200	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr12:120241200-120242200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr12:120241200-120242400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:120241200-120242600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr12:120241200-120242600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:120241200-120242800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:120241400-120242200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
45	chr12:120241400-120242200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:120241400-120242200	Active TSS	Colonic Mucosa	Colon
47	chr12:120241400-120242400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:120241400-120242600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:120241400-120242600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr12:120241400-120242600	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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