Variant report

Variant	rs558896759
Chromosome Location	chr2:32235879-32235880
allele	A/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	REST	chr2:32235781-32235947	GM12878	blood:	n/a	n/a
2	SP1	chr2:32235201-32236675	A549	lung:	n/a	chr2:32235436-32235445 chr2:32236119-32236133 chr2:32236170-32236184 chr2:32236171-32236180 chr2:32235949-32235962 chr2:32236122-32236133 chr2:32236169-32236181 chr2:32236125-32236139 chr2:32236169-32236181
3	POLR2A	chr2:32235183-32237099	PANC-1	pancreas:	n/a	n/a
4	EP300	chr2:32235756-32236311	SK-N-SH_RA	brain:	n/a	n/a
5	MYC	chr2:32235849-32236449	K562	blood:	n/a	n/a
6	CTCF	chr2:32235840-32235990	Caco-2	colon:	n/a	chr2:32235908-32235921
7	SP1	chr2:32235774-32236607	GM12878	blood:	n/a	chr2:32236119-32236133 chr2:32236170-32236184 chr2:32236171-32236180 chr2:32235949-32235962 chr2:32236122-32236133 chr2:32236169-32236181 chr2:32236125-32236139 chr2:32236169-32236181
8	TAF1	chr2:32235681-32236474	ECC-1	luminal epithelium:	n/a	n/a
9	ETS1	chr2:32235767-32236402	K562	blood:	n/a	chr2:32236186-32236193 chr2:32236171-32236182
10	RAD21	chr2:32235738-32236290	H1-hESC	embryonic stem cell:	n/a	n/a
11	NFIC	chr2:32235792-32236547	HepG2	liver:	n/a	n/a
12	CBX3	chr2:32235781-32236759	HCT-116	colon:	n/a	n/a
13	NRF1	chr2:32235851-32236399	GM12878	blood:	n/a	chr2:32236037-32236048 chr2:32236136-32236145
14	TAF1	chr2:32235762-32236399	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr2:32235215-32236461	MCF10A-Er-Src	breast:	n/a	n/a
16	YY1	chr2:32235770-32236641	GM12878	blood:	n/a	n/a
17	TEAD4	chr2:32235785-32236707	K562	blood:	n/a	n/a
18	TAF1	chr2:32235755-32236357	HepG2	liver:	n/a	n/a
19	MYC	chr2:32235751-32236576	Hela-S3	cervix:	n/a	n/a
20	REST	chr2:32235808-32236670	A549	lung:	n/a	chr2:32236170-32236183
21	YY1	chr2:32235743-32236402	HepG2	liver:	n/a	n/a
22	RCOR1	chr2:32235788-32236618	Hela-S3	cervix:	n/a	n/a
23	GABPA	chr2:32235458-32236418	K562	blood:	n/a	chr2:32236136-32236145
24	ZEB1	chr2:32235847-32236239	GM12878	blood:	n/a	n/a
25	PML	chr2:32235747-32236667	K562	blood:	n/a	n/a
26	POLR2A	chr2:32235766-32236778	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr2:32234306-32236930	Raji	blood:	n/a	n/a
28	FOXP2	chr2:32235755-32236327	PFSK-1	brain:	n/a	n/a
29	YY1	chr2:32235836-32236465	K562	blood:	n/a	n/a
30	YY1	chr2:32235789-32236334	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:32234862-32236842	GM12892	blood:	n/a	n/a
32	JUND	chr2:32235766-32236587	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr2:32234610-32236509	MCF-7	breast:	n/a	n/a
34	SPI1	chr2:32235757-32236468	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:32235781-32236398	HepG2	liver:	n/a	n/a
36	RAD21	chr2:32235781-32236278	SK-N-SH_RA	brain:	n/a	n/a
37	JUND	chr2:32235811-32236739	H1-hESC	embryonic stem cell:	n/a	n/a
38	TAF1	chr2:32235802-32236409	GM12891	blood:	n/a	n/a
39	POLR2A	chr2:32235779-32236455	HepG2	liver:	n/a	n/a
40	CREB1	chr2:32235642-32236629	HepG2	liver:	n/a	n/a
41	NFIC	chr2:32235754-32236434	GM12878	blood:	n/a	n/a
42	SP1	chr2:32235759-32236437	HepG2	liver:	n/a	chr2:32236119-32236133 chr2:32236170-32236184 chr2:32236171-32236180 chr2:32235949-32235962 chr2:32236122-32236133 chr2:32236169-32236181 chr2:32236125-32236139 chr2:32236169-32236181
43	TAF1	chr2:32235750-32236344	K562	blood:	n/a	n/a
44	POLR2A	chr2:32235835-32236496	HepG2	liver:	n/a	n/a
45	E2F6	chr2:32235748-32236524	A549	lung:	n/a	n/a
46	SIN3AK20	chr2:32235779-32236341	PFSK-1	brain:	n/a	n/a
47	POLR2A	chr2:32234312-32236987	GM18505	blood:	n/a	n/a
48	EP300	chr2:32235848-32236580	GM12878	blood:	n/a	n/a
49	BCLAF1	chr2:32235738-32236601	GM12878	blood:	n/a	n/a
50	E2F6	chr2:32235840-32236433	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:32233869..32239615-chr2:32259766..32267170,13	K562	blood:
2	chr2:32232898..32237970-chr2:32287390..32290443,5	K562	blood:
3	chr2:32233185..32238105-chr2:32388775..32395245,11	K562	blood:
4	chr2:32231133..32238127-chr2:32263164..32266706,7	MCF-7	breast:
5	chr2:32077309..32079033-chr2:32235796..32237678,2	K562	blood:
6	chr2:32234641..32236375-chr2:32389314..32391737,5	MCF-7	breast:
7	chr2:32166637..32169522-chr2:32234606..32236345,2	K562	blood:
8	chr2:32233242..32236257-chr2:32247330..32249765,3	MCF-7	breast:
9	chr17:56063594..56066516-chr2:32234123..32236602,2	MCF-7	breast:
10	chr2:32235559..32236383-chr5:43121008..43121950,2	Hela-S3	cervix:
11	chr2:32233050..32238839-chr2:32262715..32266551,10	MCF-7	breast:
12	chr2:32233869..32235900-chr2:32286911..32289660,3	K562	blood:
13	chr2:32234491..32236283-chr2:32581671..32583851,2	MCF-7	breast:
14	chr2:32233309..32238481-chr2:32286150..32290599,7	MCF-7	breast:
15	chr1:210547155..210547688-chr2:32235666..32236437,2	Hela-S3	cervix:
16	chr2:32234151..32237531-chr2:32262421..32266825,7	K562	blood:
17	chr1:227916225..227917863-chr2:32234372..32236417,2	MCF-7	breast:
18	chr2:32235154..32237462-chr2:32390889..32392468,2	MCF-7	breast:
19	chr1:45285087..45285958-chr2:32235554..32236249,2	HCT-116	colon:
20	chr2:32233077..32237611-chr2:32388376..32395245,10	K562	blood:

Variant related genes	Relation type
ENSG00000271228	TF binding region
MEMO1	TF binding region
ENSG00000273165	Chromatin interaction
ENSG00000021574	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000152683	Chromatin interaction
ENSG00000136451	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000115760	Chromatin interaction
ENSG00000200972	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000162959	Chromatin interaction
ENSG00000162961	Chromatin interaction
ENSG00000272716	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	nsv532648	chr2:31591498-32312698	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv949102	chr2:32030307-33011548	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv3416925	chr2:32233648-32236796	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	esv3339024	chr2:32233873-32237321	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr2:32233200-32236200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:32233200-32236200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr2:32233400-32236200	Active TSS	Colonic Mucosa	Colon
4	chr2:32233400-32236200	Active TSS	HSMM	muscle
5	chr2:32233400-32236400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:32233400-32236600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:32233400-32236600	Active TSS	Fetal Intestine Large	intestine
8	chr2:32233600-32236200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr2:32233600-32236200	Active TSS	Muscle Satellite Cultured Cells	--
10	chr2:32233600-32236400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:32233600-32236400	Active TSS	Stomach Smooth Muscle	stomach
12	chr2:32233600-32236600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:32233600-32236600	Active TSS	Right Ventricle	heart
14	chr2:32233600-32236600	Active TSS	GM12878-XiMat	blood
15	chr2:32233600-32236600	Active TSS	HSMMtube	muscle
16	chr2:32233600-32236800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:32233600-32236800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:32233600-32236800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr2:32233600-32236800	Active TSS	Fetal Muscle Leg	muscle
20	chr2:32233800-32236200	Active TSS	Fetal Muscle Trunk	muscle
21	chr2:32233800-32236200	Active TSS	HMEC	breast
22	chr2:32233800-32236200	Active TSS	NHEK	skin
23	chr2:32233800-32236400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr2:32233800-32236600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:32233800-32236800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr2:32234000-32236200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:32234000-32236200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr2:32234000-32236200	Active TSS	Fetal Intestine Small	intestine
29	chr2:32234000-32236200	Active TSS	Fetal Thymus	thymus
30	chr2:32234000-32236400	Active TSS	Fetal Stomach	stomach
31	chr2:32234000-32236600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr2:32234000-32236600	Active TSS	Fetal Brain Female	brain
33	chr2:32234000-32236600	Active TSS	Ovary	ovary
34	chr2:32234000-32236600	Active TSS	Psoas Muscle	Psoas
35	chr2:32234000-32236600	Active TSS	Right Atrium	heart
36	chr2:32234000-32236800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:32234000-32237000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:32234000-32237200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr2:32234200-32236200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:32234200-32236200	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr2:32234200-32236200	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr2:32234200-32236200	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr2:32234200-32236200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:32234200-32236200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:32234200-32236200	Active TSS	Liver	Liver
46	chr2:32234200-32236200	Active TSS	Brain Cingulate Gyrus	brain
47	chr2:32234200-32236200	Active TSS	Duodenum Mucosa	Duodenum
48	chr2:32234200-32236200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr2:32234200-32236200	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr2:32234200-32236200	Active TSS	HUVEC	blood vessel

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