Variant report

Variant	rs13421393
Chromosome Location	chr2:233755870-233755871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:64)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:64 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF1	chr2:233755415-233756275	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr2:233755425-233756683	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr2:233755316-233756582	ECC-1	luminal epithelium:	n/a	chr2:233755415-233755428
4	MAX	chr2:233755575-233756096	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr2:233755444-233756117	MCF-7	breast:	n/a	n/a
6	POLR2A	chr2:233755586-233755924	H1-hESC	embryonic stem cell:	n/a	n/a
7	USF1	chr2:233755083-233756305	HCT-116	colon:	n/a	n/a
8	EP300	chr2:233755606-233756054	T-47D	breast:	n/a	n/a
9	POLR2A	chr2:233755525-233756033	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr2:233755679-233755961	H1-hESC	embryonic stem cell:	n/a	n/a
11	TEAD4	chr2:233755434-233755950	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr2:233755481-233756188	MCF-7	breast:	n/a	n/a
13	ELF1	chr2:233755685-233755946	K562	blood:	n/a	chr2:233755850-233755863
14	ZNF263	chr2:233755530-233756411	HEK293-T-REx	kidney:	n/a	chr2:233756257-233756266
15	POLR2A	chr2:233755417-233756104	HCT-116	colon:	n/a	n/a
16	MAZ	chr2:233755486-233755886	K562	blood:	n/a	n/a
17	ZNF143	chr2:233755494-233756063	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr2:233755469-233756608	ECC-1	luminal epithelium:	n/a	n/a
19	TEAD4	chr2:233755384-233756157	ECC-1	luminal epithelium:	n/a	n/a
20	POLR2A	chr2:233755427-233756261	ECC-1	luminal epithelium:	n/a	n/a
21	SIN3A	chr2:233755521-233756015	H1-hESC	embryonic stem cell:	n/a	n/a
22	TEAD4	chr2:233755320-233756131	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr2:233755450-233756285	HepG2	liver:	n/a	n/a
24	MAX	chr2:233755559-233756072	NB4	blood:	n/a	n/a
25	MYC	chr2:233755689-233755988	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr2:233755515-233756113	MCF-7	breast:	n/a	n/a
27	MYC	chr2:233755763-233755940	MCF-7	breast:	n/a	n/a
28	MXI1	chr2:233755618-233756017	H1-hESC	embryonic stem cell:	n/a	n/a
29	USF1	chr2:233755401-233756253	ECC-1	luminal epithelium:	n/a	n/a
30	USF2	chr2:233755582-233755932	Hela-S3	cervix:	n/a	chr2:233755748-233755759
31	TCF7L2	chr2:233755552-233756111	HCT-116	colon:	n/a	n/a
32	USF1	chr2:233755374-233756164	H1-hESC	embryonic stem cell:	n/a	n/a
33	TCF12	chr2:233755332-233756267	ECC-1	luminal epithelium:	n/a	n/a
34	TCF12	chr2:233755381-233756194	ECC-1	luminal epithelium:	n/a	n/a
35	USF1	chr2:233755567-233755899	K562	blood:	n/a	n/a
36	YY1	chr2:233755601-233755942	HCT-116	colon:	n/a	n/a
37	TAF1	chr2:233755589-233755967	H1-hESC	embryonic stem cell:	n/a	n/a
38	STAT3	chr2:233755820-233755901	MCF10A-Er-Src	breast:	n/a	n/a
39	BHLHE40	chr2:233755560-233756094	K562	blood:	n/a	n/a
40	RAD21	chr2:233755454-233756266	ECC-1	luminal epithelium:	n/a	n/a
41	TAF1	chr2:233755431-233756137	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr2:233755348-233756364	ECC-1	luminal epithelium:	n/a	n/a
43	MAZ	chr2:233755641-233755935	Hela-S3	cervix:	n/a	n/a
44	TBP	chr2:233755626-233756133	H1-hESC	embryonic stem cell:	n/a	n/a
45	MYC	chr2:233755755-233755885	K562	blood:	n/a	n/a
46	ELF1	chr2:233755742-233755943	K562	blood:	n/a	chr2:233755850-233755863
47	EP300	chr2:233755641-233755985	T-47D	breast:	n/a	n/a
48	MYC	chr2:233755667-233755965	MCF-7	breast:	n/a	n/a
49	MAX	chr2:233755530-233755906	K562	blood:	n/a	n/a
50	FOXA1	chr2:233755641-233756008	T-47D	breast:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:233739669..233741368-chr2:233754744..233756796,2	MCF-7	breast:
2	chr2:233748378..233751543-chr2:233754163..233756692,4	MCF-7	breast:
3	chr2:233744737..233747188-chr2:233755867..233757866,2	MCF-7	breast:

No data

Variant related genes	Relation type
NGEF	TF binding region
ENSG00000066248	Chromatin interaction
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10185281	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10201344	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10205567	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10208298	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10209652	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10221688	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12477794	1.00[YRI][hapmap]
rs13382726	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13391541	0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13398944	0.83[AMR][1000 genomes]
rs13399533	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13409355	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13414498	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13420824	1.00[AMR][1000 genomes]
rs13430365	0.91[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28550401	0.83[AMR][1000 genomes]
rs28570372	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7355380	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv984452	chr2:233725452-233762965	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv999116	chr2:233733352-233759864	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1007029	chr2:233733352-233760519	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv536179	chr2:233735380-233757170	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233743200-233759600	Strong transcription	Duodenum Mucosa	Duodenum
2	chr2:233745600-233759800	Strong transcription	Liver	Liver
3	chr2:233749400-233766000	Weak transcription	A549	lung
4	chr2:233750600-233759800	Strong transcription	HepG2	liver
5	chr2:233750800-233761000	Weak transcription	Stomach Mucosa	stomach
6	chr2:233751000-233766000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:233751200-233758400	Weak transcription	Fetal Brain Male	brain
8	chr2:233753200-233757200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:233753400-233756400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:233754400-233756200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:233754400-233756200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:233754800-233756200	Enhancers	H1 Cell Line	embryonic stem cell
13	chr2:233754800-233756800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:233755000-233756600	Enhancers	Spleen	Spleen
15	chr2:233755200-233756200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:233755200-233756400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr2:233755400-233756000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr2:233755400-233756000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr2:233755400-233756200	Bivalent Enhancer	Placenta	Placenta
20	chr2:233755400-233756200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
21	chr2:233755400-233756600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:233755400-233756600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:233755400-233756800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:233755400-233756800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:233755400-233757000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr2:233755400-233757000	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr2:233755400-233759800	Strong transcription	Colonic Mucosa	Colon
28	chr2:233755600-233756000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:233755600-233756000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
30	chr2:233755600-233756000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:233755600-233756000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr2:233755600-233756000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:233755600-233756000	Enhancers	Primary B cells from peripheral blood	blood
34	chr2:233755600-233756000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:233755600-233756000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:233755600-233756000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
37	chr2:233755600-233756000	Enhancers	Left Ventricle	heart
38	chr2:233755600-233756000	Flanking Active TSS	K562	blood
39	chr2:233755600-233756200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:233755600-233756200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr2:233755600-233756200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr2:233755600-233756200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr2:233755600-233756200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:233755600-233756200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:233755600-233756200	Enhancers	Brain Germinal Matrix	brain
46	chr2:233755600-233756200	Flanking Active TSS	Ovary	ovary
47	chr2:233755600-233756200	Bivalent Enhancer	Right Ventricle	heart
48	chr2:233755600-233756200	Enhancers	NHLF	lung
49	chr2:233755600-233756400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr2:233755600-233756400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin

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