Variant report

Variant	rs555989978
Chromosome Location	chr4:90032250-90032251
allele	C/T
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	POLR2A	chr4:90032026-90033501	GM18505	blood:	n/a	n/a
2	POLR2A	chr4:90031952-90033122	GM18526	blood:	n/a	n/a
3	CTCF	chr4:90032230-90032321	HepG2	liver:	n/a	n/a
4	MYBL2	chr4:90032177-90032794	HepG2	liver:	n/a	n/a
5	IRF1	chr4:90032086-90032882	K562	blood:	n/a	chr4:90032629-90032643
6	YY1	chr4:90032134-90033057	GM12878	blood:	n/a	chr4:90032571-90032582 chr4:90032633-90032642 chr4:90032631-90032645
7	MAX	chr4:90031662-90033107	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
8	TRIM28	chr4:90032109-90032684	K562	blood:	n/a	n/a
9	CTCF	chr4:90032175-90032629	MCF-7	breast:	n/a	n/a
10	ZC3H11A	chr4:90032093-90032536	K562	blood:	n/a	n/a
11	SIN3AK20	chr4:90032106-90032591	PFSK-1	brain:	n/a	n/a
12	SIN3AK20	chr4:90031811-90033148	MCF-7	breast:	n/a	n/a
13	RAD21	chr4:90032249-90032632	GM12878	blood:	n/a	n/a
14	POLR2A	chr4:90032083-90033086	K562	blood:	n/a	n/a
15	CTCF	chr4:90032095-90032642	HepG2	liver:	n/a	n/a
16	BHLHE40	chr4:90032021-90033369	GM12878	blood:	n/a	chr4:90032093-90032109
17	SETDB1	chr4:90031866-90033084	K562	blood:	n/a	n/a
18	CTCF	chr4:90032200-90032350	RPTEC	kidney:	n/a	n/a
19	CTCF	chr4:90032109-90032626	GM19239	blood:	n/a	n/a
20	FOXA2	chr4:90032023-90032732	A549	lung:	n/a	n/a
21	SIN3AK20	chr4:90032126-90032381	A549	lung:	n/a	n/a
22	BHLHE40	chr4:90032103-90032992	HepG2	liver:	n/a	n/a
23	POLR2A	chr4:90032026-90032528	GM12878	blood:	n/a	n/a
24	MXI1	chr4:90031599-90033231	GM12878	blood:	n/a	chr4:90031789-90031804
25	MAX	chr4:90031818-90033188	HepG2	liver:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
26	TCF12	chr4:90032096-90032573	GM12878	blood:	n/a	n/a
27	EP300	chr4:90032131-90033018	GM12878	blood:	n/a	chr4:90032597-90032613
28	SIN3AK20	chr4:90032167-90032986	SK-N-SH	brain:	n/a	n/a
29	SP1	chr4:90032116-90032841	GM12878	blood:	n/a	chr4:90032597-90032606 chr4:90032632-90032641 chr4:90032633-90032642 chr4:90032632-90032646 chr4:90032632-90032642 chr4:90032567-90032581 chr4:90032568-90032577 chr4:90032632-90032641 chr4:90032687-90032701 chr4:90032632-90032642 chr4:90032595-90032607 chr4:90032631-90032643 chr4:90032567-90032576 chr4:90032566-90032578 chr4:90032631-90032643 chr4:90032566-90032578
30	POLR2A	chr4:90031925-90033139	GM19193	blood:	n/a	n/a
31	USF1	chr4:90032080-90032726	ECC-1	luminal epithelium:	n/a	chr4:90032093-90032109
32	RELA	chr4:90031877-90033556	GM10847	blood:	n/a	n/a
33	BHLHE40	chr4:90031774-90033235	K562	blood:	n/a	chr4:90032093-90032109 chr4:90031987-90032003
34	YY1	chr4:90032108-90032982	GM12878	blood:	n/a	chr4:90032571-90032582 chr4:90032633-90032642 chr4:90032631-90032645
35	CTCF	chr4:90032097-90032595	K562	blood:	n/a	n/a
36	EP300	chr4:90032219-90033272	GM12878	blood:	n/a	chr4:90032597-90032613
37	MAX	chr4:90031702-90033805	A549	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
38	EBF1	chr4:90031991-90032947	GM12878	blood:	n/a	chr4:90032399-90032410
39	CBX3	chr4:90031993-90033181	K562	blood:	n/a	n/a
40	CTCF	chr4:90032129-90032591	A549	lung:	n/a	n/a
41	CTCF	chr4:90032033-90032804	K562	blood:	n/a	n/a
42	EP300	chr4:90031929-90033121	ECC-1	luminal epithelium:	n/a	chr4:90032597-90032613
43	FOXM1	chr4:90032201-90032861	GM12878	blood:	n/a	n/a
44	POLR2A	chr4:90031741-90033492	GM19099	blood:	n/a	n/a
45	E2F4	chr4:90031914-90033095	K562	blood:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
46	E2F6	chr4:90031734-90033155	H1-hESC	embryonic stem cell:	n/a	chr4:90032663-90032672 chr4:90032574-90032586 chr4:90032633-90032642 chr4:90032628-90032638
47	ZNF143	chr4:90032168-90033085	K562	blood:	n/a	n/a
48	MYC	chr4:90032143-90032780	K562	blood:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
49	EP300	chr4:90032221-90033588	K562	blood:	n/a	chr4:90032597-90032613
50	CTCF	chr4:90032240-90032390	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:89739936..89740488-chr4:90031811..90032510,2	MCF-7	breast:
2	chr4:89443831..89446134-chr4:90031080..90033028,2	K562	blood:
3	chr4:89977166..89979264-chr4:90032025..90033904,2	K562	blood:
4	chr4:89739661..89740284-chr4:90031824..90032453,2	MCF-7	breast:
5	chr4:90032248..90033146-chr6:26103791..26104616,2	Hela-S3	cervix:
6	chr4:90021012..90023295-chr4:90030744..90032396,2	K562	blood:
7	chr4:90030188..90033002-chr4:90049823..90052502,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271359	TF binding region
TIGD2	TF binding region
ENSG00000212226	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000197061	Chromatin interaction
ENSG00000145337	Chromatin interaction
ENSG00000138641	Chromatin interaction

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

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3437234	chr4:90031454-90034302	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr4:90030800-90033600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:90031000-90033400	Active TSS	Pancreas	Pancrea
3	chr4:90031200-90033000	Active TSS	Fetal Brain Female	brain
4	chr4:90031200-90033200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:90031200-90033400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:90031400-90032400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:90031400-90032400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr4:90031400-90032400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
9	chr4:90031400-90033400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr4:90031400-90033400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr4:90031400-90033600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:90031600-90032400	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
14	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr4:90031600-90032400	Flanking Active TSS	Placenta	Placenta
17	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	HepG2	liver
18	chr4:90031600-90032400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
19	chr4:90031600-90033200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr4:90031600-90033200	Active TSS	Brain Substantia Nigra	brain
21	chr4:90031600-90033200	Active TSS	Fetal Intestine Small	intestine
22	chr4:90031600-90033400	Active TSS	H9 Cell Line	embryonic stem cell
23	chr4:90031600-90033400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:90031600-90033400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr4:90031600-90033400	Active TSS	Right Atrium	heart
26	chr4:90031600-90033600	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr4:90031600-90033600	Active TSS	Placenta Amnion	Placenta Amnion
28	chr4:90031800-90032400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:90031800-90032400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:90031800-90032400	Flanking Active TSS	Colonic Mucosa	Colon
31	chr4:90031800-90032400	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr4:90031800-90032400	Flanking Bivalent TSS/Enh	NHEK	skin
33	chr4:90031800-90032800	Active TSS	Spleen	Spleen
34	chr4:90031800-90033000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
35	chr4:90031800-90033200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:90031800-90033200	Active TSS	Brain Hippocampus Middle	brain
37	chr4:90031800-90033400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr4:90031800-90033400	Active TSS	Fetal Brain Male	brain
39	chr4:90031800-90033400	Active TSS	Fetal Heart	heart
40	chr4:90031800-90033400	Active TSS	Psoas Muscle	Psoas
41	chr4:90031800-90033600	Active TSS	Aorta	Aorta
42	chr4:90031800-90033600	Active TSS	Fetal Kidney	kidney
43	chr4:90031800-90033600	Active TSS	Gastric	stomach
44	chr4:90031800-90033800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:90032000-90032400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:90032000-90032400	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr4:90032000-90032400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr4:90032000-90032400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr4:90032000-90032400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:90032000-90032400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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