Variant report

Variant	rs13392090
Chromosome Location	chr2:36580097-36580098
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:85)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:85 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:36580060-36580210	AG04450	lung:	n/a	n/a
2	BHLHE40	chr2:36580084-36580135	GM12878	blood:	n/a	n/a
3	STAT3	chr2:36579845-36580345	MCF10A-Er-Src	breast:	n/a	n/a
4	RAD21	chr2:36579016-36580163	HepG2	liver:	n/a	chr2:36579351-36579370
5	SMC3	chr2:36579942-36580253	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr2:36580040-36580190	HEEpiC	esophagus:	n/a	n/a
7	FOS	chr2:36579761-36580354	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr2:36579951-36580143	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr2:36579903-36580237	MCF10A-Er-Src	breast:	n/a	n/a
10	NFIC	chr2:36579724-36580402	SK-N-SH	brain:	n/a	n/a
11	CTCF	chr2:36580060-36580210	HepG2	liver:	n/a	n/a
12	CTCF	chr2:36580020-36580170	GM12872	blood:	n/a	n/a
13	CTCF	chr2:36580020-36580170	HBMEC	blood vessel:	n/a	n/a
14	CTCF	chr2:36580040-36580190	AG09319	gingival:	n/a	n/a
15	CTCF	chr2:36580060-36580210	HPF	lung:	n/a	n/a
16	CTCF	chr2:36579960-36580110	HCT-116	colon:	n/a	n/a
17	CTCF	chr2:36580020-36580170	HA-sp	spinal cord:	n/a	n/a
18	CTCF	chr2:36580064-36580139	Kidney_OC	kidney:	n/a	n/a
19	CTCF	chr2:36580060-36580210	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr2:36580060-36580210	AG10803	skin:	n/a	n/a
21	FOS	chr2:36579846-36580301	MCF10A-Er-Src	breast:	n/a	n/a
22	CTCF	chr2:36580060-36580210	AoAF	blood vessel:	n/a	n/a
23	CEBPB	chr2:36579878-36580241	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr2:36580000-36580150	HCFaa	heart:	n/a	n/a
25	RAD21	chr2:36579948-36580186	SK-N-SH_RA	brain:	n/a	n/a
26	BACH1	chr2:36579889-36580104	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr2:36579782-36580329	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr2:36580040-36580190	AoAF	blood vessel:	n/a	n/a
29	CTCF	chr2:36580000-36580150	HPAF	blood vessel:	n/a	n/a
30	CTCF	chr2:36579940-36580230	HRPEpiC	eye:	n/a	n/a
31	POLR2A	chr2:36579981-36580175	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr2:36580000-36580150	BJ	skin:	n/a	n/a
33	CTCF	chr2:36580020-36580170	HRE	kidney:	n/a	n/a
34	CTCF	chr2:36580060-36580210	HAc	cerebellar:	n/a	n/a
35	TCF12	chr2:36579088-36580884	SK-N-SH	brain:	n/a	n/a
36	CEBPB	chr2:36579793-36580249	IMR90	lung:	n/a	n/a
37	MAFK	chr2:36579979-36580119	HepG2	liver:	n/a	n/a
38	FOS	chr2:36579849-36580290	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr2:36580060-36580210	AG04449	skin:	n/a	n/a
40	RAD21	chr2:36578763-36580558	SK-N-SH	brain:	n/a	chr2:36579351-36579370
41	CTCF	chr2:36580000-36580150	GM12873	blood:	n/a	n/a
42	CTCF	chr2:36580020-36580170	HPF	lung:	n/a	n/a
43	EP300	chr2:36579945-36580239	HepG2	liver:	n/a	chr2:36580209-36580223
44	SMC3	chr2:36578845-36580736	SK-N-SH	brain:	n/a	n/a
45	CTCF	chr2:36580040-36580190	BJ	skin:	n/a	n/a
46	CTCF	chr2:36579960-36580110	RPTEC	kidney:	n/a	n/a
47	MYC	chr2:36579951-36580332	MCF10A-Er-Src	breast:	n/a	n/a
48	CTCF	chr2:36580060-36580210	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr2:36579980-36580130	HRE	kidney:	n/a	n/a
50	CTCF	chr2:36580040-36580190	HBMEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:36579541..36582234-chr2:36891147..36893577,3	MCF-7	breast:
2	chr2:36579431..36580979-chr2:36581786..36583464,2	MCF-7	breast:

No data

Variant related genes	Relation type
CRIM1	TF binding region
ENSG00000150938	Chromatin interaction
ENSG00000260025	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs13389698	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13405945	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4670544	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757792	chr2:36243452-36590658	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv2759040	chr2:36243452-36590658	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36577200-36580800	Enhancers	Placenta Amnion	Placenta Amnion
2	chr2:36578000-36581200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:36578200-36581200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:36578200-36581200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:36578400-36581200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:36578600-36581000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr2:36578800-36581200	Enhancers	HMEC	breast
8	chr2:36578800-36581400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:36578800-36581400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:36578800-36581400	Enhancers	NHLF	lung
11	chr2:36578800-36581600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:36579000-36580200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:36579000-36580600	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:36579000-36581600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:36579000-36581600	Enhancers	Adipose Nuclei	Adipose
16	chr2:36579000-36581600	Enhancers	Hela-S3	cervix
17	chr2:36579000-36581800	Enhancers	Fetal Heart	heart
18	chr2:36579000-36582000	Enhancers	Stomach Mucosa	stomach
19	chr2:36579200-36581400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:36579200-36582000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:36579400-36580600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:36579400-36581000	Enhancers	HSMM	muscle
23	chr2:36579600-36580200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr2:36579600-36580400	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:36579600-36580600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:36579600-36580600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:36579600-36580600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:36579600-36580600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:36579600-36580600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:36579600-36580600	Enhancers	NH-A	brain
31	chr2:36579600-36580800	Flanking Active TSS	A549	lung
32	chr2:36579600-36581200	Enhancers	NHDF-Ad	bronchial
33	chr2:36579600-36581400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:36579600-36581400	Enhancers	Brain Anterior Caudate	brain
35	chr2:36579600-36581600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:36579600-36581600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:36579600-36581600	Enhancers	Brain Substantia Nigra	brain
38	chr2:36579600-36581600	Enhancers	Fetal Kidney	kidney
39	chr2:36579600-36582000	Enhancers	Primary B cells from cord blood	blood
40	chr2:36579800-36580200	Flanking Active TSS	HepG2	liver
41	chr2:36579800-36580400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:36579800-36580600	Flanking Active TSS	Osteobl	bone
43	chr2:36579800-36580800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:36579800-36580800	Enhancers	GM12878-XiMat	blood
45	chr2:36579800-36580800	Flanking Active TSS	HUVEC	blood vessel
46	chr2:36579800-36581400	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:36579800-36581400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:36579800-36581400	Enhancers	Placenta	Placenta
49	chr2:36579800-36581600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:36579800-36582400	Enhancers	Primary B cells from peripheral blood	blood

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