Variant report

Variant	rs1154519
Chromosome Location	chr12:122356232-122356233
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	RFX5	chr12:122356172-122356935	H1-hESC	embryonic stem cell:	n/a	chr12:122356465-122356480 chr12:122356465-122356480 chr12:122356463-122356477 chr12:122356466-122356475 chr12:122356462-122356477 chr12:122356465-122356480 chr12:122356464-122356481
2	PML	chr12:122356075-122356690	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:122355807-122356649	K562	blood:	n/a	n/a
4	MXI1	chr12:122356108-122356838	GM12878	blood:	n/a	chr12:122356466-122356481
5	TBP	chr12:122356207-122356585	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr12:122355934-122356856	HCT-116	colon:	n/a	chr12:122356083-122356093
7	CTCF	chr12:122356228-122356497	GM10266	blood:	n/a	chr12:122356368-122356381
8	RUNX3	chr12:122356125-122356640	GM12878	blood:	n/a	n/a
9	ELF1	chr12:122355817-122356839	GM12878	blood:	n/a	chr12:122356751-122356763 chr12:122356116-122356128 chr12:122356449-122356458
10	POLR2A	chr12:122355922-122356687	GM12892	blood:	n/a	n/a
11	RAD21	chr12:122355970-122356709	ECC-1	luminal epithelium:	n/a	chr12:122356083-122356093
12	EP300	chr12:122356034-122356566	GM12878	blood:	n/a	chr12:122356073-122356080
13	CTCF	chr12:122356164-122356524	Lung_OC	lung:	n/a	chr12:122356368-122356381
14	POLR2A	chr12:122356015-122356718	MCF-7	breast:	n/a	n/a
15	SRF	chr12:122355938-122356793	MCF-7	breast:	n/a	n/a
16	CTCF	chr12:122356160-122356310	HAc	cerebellar:	n/a	n/a
17	SRF	chr12:122356186-122356639	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD2	chr12:122356079-122356619	GM12878	blood:	n/a	n/a
19	RFX5	chr12:122355885-122356812	GM12878	blood:	n/a	chr12:122356465-122356480 chr12:122356465-122356480 chr12:122356463-122356477 chr12:122356466-122356475 chr12:122356462-122356477 chr12:122356465-122356480 chr12:122356464-122356481
20	RCOR1	chr12:122356202-122356635	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:122356155-122356789	HUVEC	blood vessel:	n/a	n/a
22	RAD21	chr12:122356115-122356967	H1-hESC	embryonic stem cell:	n/a	n/a
23	SRF	chr12:122356017-122356817	MCF-7	breast:	n/a	n/a
24	RUNX3	chr12:122356105-122356613	GM12878	blood:	n/a	n/a
25	ELF1	chr12:122356030-122356758	MCF-7	breast:	n/a	chr12:122356116-122356128 chr12:122356449-122356458
26	CREB1	chr12:122356127-122356731	GM12878	blood:	n/a	n/a
27	FOXM1	chr12:122355991-122356613	GM12878	blood:	n/a	n/a
28	RFX5	chr12:122355894-122356806	IMR90	lung:	n/a	chr12:122356465-122356480 chr12:122356465-122356480 chr12:122356463-122356477 chr12:122356466-122356475 chr12:122356462-122356477 chr12:122356465-122356480 chr12:122356464-122356481
29	POLR2A	chr12:122356112-122356613	GM12892	blood:	n/a	n/a
30	MTA3	chr12:122355977-122356634	GM12878	blood:	n/a	n/a
31	RAD21	chr12:122355967-122356801	HCT-116	colon:	n/a	chr12:122356083-122356093
32	TEAD4	chr12:122356186-122356630	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:122356223-122356515	Medullo	brain:	n/a	chr12:122356368-122356381
34	USF1	chr12:122356196-122356577	GM12878	blood:	n/a	chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
35	USF1	chr12:122356027-122356810	HCT-116	colon:	n/a	chr12:122356750-122356766 chr12:122356406-122356419 chr12:122356408-122356417 chr12:122356409-122356418 chr12:122356407-122356416 chr12:122356408-122356417
36	POLR2A	chr12:122356191-122356724	HUVEC	blood vessel:	n/a	n/a
37	MAX	chr12:122355876-122356699	H1-hESC	embryonic stem cell:	n/a	chr12:122356113-122356120 chr12:122356408-122356417 chr12:122356466-122356475 chr12:122356632-122356641
38	ZNF143	chr12:122356193-122356567	GM12878	blood:	n/a	n/a
39	SP1	chr12:122356220-122356621	GM12878	blood:	n/a	n/a
40	JUN	chr12:122356232-122356479	H1-hESC	embryonic stem cell:	n/a	n/a
41	SRF	chr12:122356175-122356595	H1-hESC	embryonic stem cell:	n/a	n/a
42	CREB1	chr12:122356140-122356744	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3AK20	chr12:122356171-122356898	PANC-1	pancreas:	n/a	n/a
44	RAD21	chr12:122356115-122356572	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr12:122356122-122356599	H1-hESC	embryonic stem cell:	n/a	chr12:122356529-122356542 chr12:122356544-122356557 chr12:122356368-122356381
46	SIN3A	chr12:122356118-122356932	H1-hESC	embryonic stem cell:	n/a	n/a
47	WRNIP1	chr12:122356190-122356322	GM12878	blood:	n/a	n/a
48	SMC3	chr12:122356177-122356562	GM12878	blood:	n/a	chr12:122356371-122356381 chr12:122356367-122356381
49	NFE2	chr12:122356215-122356573	GM12878	blood:	n/a	chr12:122356408-122356417
50	CTCF	chr12:122356208-122356509	GM12878	blood:	n/a	chr12:122356368-122356381

No.	Distal block	Cell Line	Cell type
1	chr12:122352837..122354864-chr12:122355521..122357983,3	MCF-7	breast:
2	chr12:122354300..122356847-chr12:122457161..122460061,2	K562	blood:
3	chr12:122353848..122356586-chr12:122614343..122616936,2	MCF-7	breast:
4	chr12:122325289..122328252-chr12:122355129..122358130,3	MCF-7	breast:
5	chr12:122239660..122241230-chr12:122355073..122357147,2	MCF-7	breast:
6	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
7	chr12:122343793..122346484-chr12:122354637..122356922,2	MCF-7	breast:
8	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
9	chr12:122355691..122357856-chr12:122357924..122360707,2	MCF-7	breast:

Variant related genes	Relation type
WDR66	TF binding region
ENSG00000110801	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000239082	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1144030	0.83[AMR][1000 genomes]
rs1154517	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1168658	0.94[YRI][hapmap]
rs1168662	1.00[AMR][1000 genomes]
rs1177573	0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs1627963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1630699	0.85[YRI][hapmap]
rs1667581	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1678958	0.83[AMR][1000 genomes]
rs1678968	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1720037	0.82[YRI][hapmap]
rs1720069	0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2620342	0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2707064	0.83[AMR][1000 genomes]
rs4069666	0.94[YRI][hapmap]
rs483416	0.94[YRI][hapmap]
rs830128	0.83[AMR][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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122332000-122356600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:122341600-122356600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:122344400-122356400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:122353200-122356400	Strong transcription	HepG2	liver
5	chr12:122353400-122356400	Strong transcription	Ovary	ovary
6	chr12:122353600-122356600	Genic enhancers	HSMMtube	muscle
7	chr12:122353600-122356800	Strong transcription	A549	lung
8	chr12:122354200-122356400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:122354200-122363000	Weak transcription	Small Intestine	intestine
10	chr12:122354600-122356400	Strong transcription	HMEC	breast
11	chr12:122354800-122356600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:122355000-122357600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:122355000-122357600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:122355200-122357400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:122355600-122356400	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr12:122355600-122364800	Weak transcription	K562	blood
17	chr12:122355800-122356400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:122355800-122356400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr12:122355800-122356400	Enhancers	Lung	lung
20	chr12:122355800-122356400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr12:122355800-122356800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr12:122355800-122356800	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr12:122355800-122357000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:122355800-122357000	Active TSS	Rectal Smooth Muscle	rectum
25	chr12:122355800-122357000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr12:122356000-122356400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:122356000-122356400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr12:122356000-122356400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr12:122356000-122356400	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:122356000-122356400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:122356000-122356400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:122356000-122356400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
33	chr12:122356000-122356400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr12:122356000-122356400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr12:122356000-122356400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:122356000-122356400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr12:122356000-122356400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
39	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
40	chr12:122356000-122356400	Flanking Active TSS	Brain Cingulate Gyrus	brain
41	chr12:122356000-122356400	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr12:122356000-122356400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
44	chr12:122356000-122356400	Flanking Active TSS	Fetal Brain Male	brain
45	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
46	chr12:122356000-122356400	Genic enhancers	Placenta	Placenta
47	chr12:122356000-122356400	Enhancers	Placenta Amnion	Placenta Amnion
48	chr12:122356000-122356400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
50	chr12:122356000-122356400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach

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