Variant report

Variant	rs1154517
Chromosome Location	chr12:122354705-122354706
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:122354541-122355168	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr12:122354564-122355211	A549	lung:	n/a	n/a
3	RAD21	chr12:122354697-122355009	Hela-S3	cervix:	n/a	n/a
4	CTCF	chr12:122354673-122354974	T-47D	breast:	n/a	n/a
5	RAD21	chr12:122354696-122354953	GM12878	blood:	n/a	n/a
6	CTCF	chr12:122354700-122354850	NHEK	skin:	n/a	n/a
7	RAD21	chr12:122354665-122354992	H1-hESC	embryonic stem cell:	n/a	n/a
8	SPI1	chr12:122354604-122355077	HL-60	blood:	n/a	n/a
9	CTCF	chr12:122354700-122354850	HFF-Myc	foreskin:	n/a	n/a
10	RAD21	chr12:122354689-122355039	IMR90	lung:	n/a	n/a
11	RAD21	chr12:122354640-122355090	A549	lung:	n/a	n/a
12	CTCF	chr12:122354560-122354710	NHEK	skin:	n/a	n/a
13	RAD21	chr12:122354554-122355165	A549	lung:	n/a	n/a
14	SMC3	chr12:122354440-122355193	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr12:122354680-122354830	GM06990	blood:	n/a	n/a
16	CTCF	chr12:122354600-122354750	GM12867	blood:	n/a	n/a
17	CTCF	chr12:122354662-122354974	A549	lung:	n/a	n/a
18	RAD21	chr12:122354687-122355004	SK-N-SH_RA	brain:	n/a	n/a
19	RAD21	chr12:122354675-122354997	GM12878	blood:	n/a	n/a
20	CTCF	chr12:122354700-122354850	HCM	heart:	n/a	n/a
21	CTCF	chr12:122354679-122355014	GM12878	blood:	n/a	n/a
22	CTCF	chr12:122354525-122355207	SK-N-SH	brain:	n/a	n/a
23	CTCF	chr12:122354680-122354830	GM12870	blood:	n/a	n/a
24	CTCF	chr12:122354680-122354830	WI-38	lung:	n/a	n/a
25	CTCF	chr12:122354700-122354850	HMF	breast:	n/a	n/a
26	CTCF	chr12:122354649-122355006	A549	lung:	n/a	n/a
27	CTCF	chr12:122354700-122354850	BE2_C	brain:	n/a	n/a
28	RAD21	chr12:122354647-122355039	HepG2	liver:	n/a	n/a
29	CTCF	chr12:122354675-122355019	IMR90	lung:	n/a	n/a
30	RAD21	chr12:122354647-122355043	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122354300..122356847-chr12:122457161..122460061,2	K562	blood:
2	chr12:122353848..122356586-chr12:122614343..122616936,2	MCF-7	breast:
3	chr12:122331116..122333896-chr12:122352806..122354784,2	MCF-7	breast:
4	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
5	chr12:122343793..122346484-chr12:122354637..122356922,2	MCF-7	breast:
6	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
7	chr12:122241012..122243645-chr12:122353946..122355842,2	MCF-7	breast:
8	chr12:122352837..122354864-chr12:122355521..122357983,3	MCF-7	breast:

No data

Variant related genes	Relation type
WDR66	TF binding region
ENSG00000139718	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000110987	Chromatin interaction
ENSG00000255856	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000175727	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]
rs1154514	0.82[YRI][hapmap]
rs1154519	0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1168658	0.95[YRI][hapmap]
rs1168662	1.00[AMR][1000 genomes]
rs1177573	0.83[AMR][1000 genomes]
rs1627963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
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]
rs1720068	0.86[YRI][hapmap]
rs1720069	0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2620342	0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2707064	0.83[AMR][1000 genomes]
rs4069666	1.00[YRI][hapmap]
rs483416	0.95[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122328200-122355600	Weak transcription	Fetal Brain Male	brain
2	chr12:122328400-122355600	Strong transcription	Fetal Stomach	stomach
3	chr12:122329600-122355800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:122329600-122355800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:122329800-122355000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:122330400-122355800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:122331000-122355000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:122331600-122355600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:122332000-122356600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr12:122332400-122355600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:122332400-122355600	Strong transcription	Fetal Intestine Small	intestine
12	chr12:122332400-122355800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:122332600-122355400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:122332600-122355600	Strong transcription	Fetal Intestine Large	intestine
15	chr12:122332800-122355000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:122332800-122355400	Strong transcription	Liver	Liver
17	chr12:122332800-122355600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr12:122333000-122356000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:122336400-122356000	Strong transcription	Adipose Nuclei	Adipose
20	chr12:122338000-122356000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:122341000-122356000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:122341400-122355800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:122341600-122356000	Weak transcription	Fetal Heart	heart
24	chr12:122341600-122356600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:122341800-122355600	Weak transcription	Stomach Mucosa	stomach
26	chr12:122342200-122356000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:122344000-122355800	Strong transcription	Brain Germinal Matrix	brain
28	chr12:122344200-122355800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr12:122344400-122356400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:122345400-122356000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:122345600-122355600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:122345600-122355800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:122346200-122355800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:122346600-122356000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr12:122347000-122355600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:122347000-122355800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:122347200-122355600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:122347200-122356000	Weak transcription	Psoas Muscle	Psoas
39	chr12:122347800-122356000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:122347800-122356000	Weak transcription	Brain Angular Gyrus	brain
41	chr12:122348000-122355800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:122348800-122355200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr12:122349200-122355600	Strong transcription	Lung	lung
44	chr12:122349400-122356000	Weak transcription	Fetal Kidney	kidney
45	chr12:122350000-122355800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:122350000-122356000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:122350000-122356200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:122350200-122355600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:122350600-122355800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:122350600-122355800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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