Variant report

Variant	rs554204056
Chromosome Location	chr4:91048578-91048579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:160)
CpG islands
(count:183)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:160 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:91048425-91048754	Hela-S3	cervix:	n/a	n/a
2	TAF1	chr4:91048421-91048920	H1-neurons	neurons:	n/a	n/a
3	TCF3	chr4:91048452-91048681	GM12878	blood:	n/a	n/a
4	ELF1	chr4:91048288-91049254	GM12878	blood:	n/a	chr4:91048461-91048473 chr4:91049040-91049052
5	FOXA1	chr4:91048432-91048809	T-47D	breast:	n/a	n/a
6	POLR2A	chr4:91048392-91048872	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:91048271-91049914	ECC-1	luminal epithelium:	n/a	n/a
8	RAD21	chr4:91048314-91048955	SK-N-SH_RA	brain:	n/a	n/a
9	POLR2A	chr4:91048428-91048882	Hela-S3	cervix:	n/a	n/a
10	BHLHE40	chr4:91048397-91049079	GM12878	blood:	n/a	chr4:91049042-91049058
11	POLR2A	chr4:91048301-91049438	ECC-1	luminal epithelium:	n/a	n/a
12	MYC	chr4:91048324-91049350	MCF-7	breast:	n/a	chr4:91049221-91049230
13	PML	chr4:91048404-91048907	GM12878	blood:	n/a	n/a
14	USF1	chr4:91048432-91049214	ECC-1	luminal epithelium:	n/a	chr4:91049077-91049093 chr4:91049042-91049058
15	POLR2A	chr4:91048410-91048896	HUVEC	blood vessel:	n/a	n/a
16	GATA2	chr4:91047829-91049296	SH-SY5Y	brain:	n/a	chr4:91049230-91049240
17	POLR2A	chr4:91048249-91049524	ProgFib	skin:	n/a	n/a
18	KAP1	chr4:91048220-91048858	U2OS	brain:	n/a	n/a
19	CTCF	chr4:91048480-91048630	SK-N-SH_RA	brain:	n/a	n/a
20	ZNF143	chr4:91048284-91048812	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:91048435-91048811	GM12892	blood:	n/a	n/a
22	POLR2A	chr4:91048330-91049073	GM12892	blood:	n/a	n/a
23	RAD21	chr4:91048061-91049024	MCF-7	breast:	n/a	n/a
24	TAF1	chr4:91048358-91048923	MCF-7	breast:	n/a	n/a
25	POLR2A	chr4:91048434-91048827	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:91048287-91048977	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr4:91048268-91049891	GM15510	blood:	n/a	n/a
28	POLR2A	chr4:91048472-91049041	Hela-S3	cervix:	n/a	n/a
29	EP300	chr4:91048264-91050124	ECC-1	luminal epithelium:	n/a	chr4:91049258-91049274 chr4:91049272-91049281
30	CTCF	chr4:91048567-91048645	GM19240	blood:	n/a	n/a
31	POLR2A	chr4:91048233-91049369	GM12892	blood:	n/a	n/a
32	POLR2A	chr4:91048370-91049907	GM18505	blood:	n/a	n/a
33	POLR2A	chr4:91048274-91049887	HEK293	kidney:	n/a	n/a
34	KAP1	chr4:91048335-91049252	HEK293	kidney:	n/a	n/a
35	CTCF	chr4:91048520-91048670	GM12868	blood:	n/a	n/a
36	POLR2A	chr4:91048426-91048721	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr4:91048207-91049876	MCF-7	breast:	n/a	n/a
38	PML	chr4:91048309-91049040	MCF-7	breast:	n/a	n/a
39	SIN3AK20	chr4:91048246-91048982	HCT-116	colon:	n/a	n/a
40	SIN3A	chr4:91048339-91049942	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr4:91048439-91048715	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:91048517-91048625	A549	lung:	n/a	n/a
43	POLR2A	chr4:91048270-91049961	HCT-116	colon:	n/a	n/a
44	POLR2A	chr4:91048211-91050043	H1-neurons	neurons:	n/a	n/a
45	POLR2A	chr4:91048222-91050382	GM19193	blood:	n/a	n/a
46	CTCF	chr4:91048508-91048703	GM12892	blood:	n/a	n/a
47	NFIC	chr4:91048229-91049038	ECC-1	luminal epithelium:	n/a	n/a
48	TEAD4	chr4:91048188-91048834	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr4:91048322-91048935	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:91047576-91050111	H1-neurons	neurons:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:91048559-91048609	NHDF-neo	bronchial:	n/a
2	chr4:91048567-91048617	Jurkat	blood:	n/a
3	chr4:91048559-91048609	HIPEpiC	eye:	n/a
4	chr4:91048567-91048617	HCF	heart:	n/a
5	chr4:91048559-91048609	K562	blood:	n/a
6	chr4:91048557-91048607	HNPCEpiC	eye:	n/a
7	chr4:91048559-91048609	Jurkat	blood:	n/a
8	chr4:91048559-91048609	GM12878	blood:	n/a
9	chr4:91048567-91048617	GM06990	blood:	n/a
10	chr4:91048557-91048607	GM12892	blood:	n/a
11	chr4:91048559-91048609	HCM	heart:	n/a
12	chr4:91048567-91048617	HRCEpiC	kidney:	n/a
13	chr4:91048557-91048607	HPAEpiC	pulmonary alveolar:	n/a
14	chr4:91048567-91048617	PANC-1	pancreas:	n/a
15	chr4:91048559-91048609	HEEpiC	esophagus:	n/a
16	chr4:91048559-91048609	HCT-116	colon:	n/a
17	chr4:91048557-91048607	GM12891	blood:	n/a
18	chr4:91048557-91048607	MCF10A-Er-Src	breast:	n/a
19	chr4:91048557-91048607	HCF	heart:	n/a
20	chr4:91048557-91048607	NHDF-neo	bronchial:	n/a
21	chr4:91048567-91048617	GM12878	blood:	n/a
22	chr4:91048557-91048607	HRPEpiC	eye:	n/a
23	chr4:91048557-91048607	NT2-D1	testis:	n/a
24	chr4:91048557-91048607	MCF-7	breast:	n/a
25	chr4:91048557-91048607	K562	blood:	n/a
26	chr4:91048559-91048609	HMEC	breast:	n/a
27	chr4:91048559-91048609	T-47D	breast:	n/a
28	chr4:91048567-91048617	GM12891	blood:	n/a
29	chr4:91048557-91048607	AG04450	lung:	fetal
30	chr4:91048559-91048609	AG09319	gingival:	n/a
31	chr4:91048559-91048609	BJ	skin:	n/a
32	chr4:91048559-91048609	HepG2	liver:	n/a
33	chr4:91048559-91048609	SK-N-MC	brain:	n/a
34	chr4:91048557-91048607	HL-60	blood:	n/a
35	chr4:91048557-91048607	AoSMC	blood vessel:	n/a
36	chr4:91048559-91048609	GM06990	blood:	n/a
37	chr4:91048557-91048607	Hepatocyte	liver:	n/a
38	chr4:91048559-91048609	Hela-S3	cervix:	n/a
39	chr4:91048557-91048607	SAEC	small airway:	n/a
40	chr4:91048559-91048609	HEK293	kidney:	embryo
41	chr4:91048567-91048617	Hepatocyte	liver:	n/a
42	chr4:91048559-91048609	CMK	blood:	n/a
43	chr4:91048567-91048617	GM12892	blood:	n/a
44	chr4:91048567-91048617	HMEC	breast:	n/a
45	chr4:91048567-91048617	NHDF-neo	bronchial:	n/a
46	chr4:91048557-91048607	IMR90	lung:	fetal
47	chr4:91048559-91048609	NT2-D1	testis:	n/a
48	chr4:91048559-91048609	HPAEpiC	pulmonary alveolar:	n/a
49	chr4:91048559-91048609	AG04450	lung:	fetal
50	chr4:91048567-91048617	HUVEC	blood vessel:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:2058702..2060790-chr4:91048350..91050086,2	MCF-7	breast:
2	chr4:91048233..91049088-chr5:95066829..95067559,2	HCT-116	colon:
3	chr4:91048485..91049157-chr9:101983883..101984451,2	Hela-S3	cervix:
4	chr1:33815262..33816159-chr4:91048253..91048899,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
CCSER1	TF binding region
CCSER1	CpG island
ENSG00000119523	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000183971	Chromatin interaction
ENSG00000134686	Chromatin interaction
ENSG00000167962	Chromatin interaction
ENSG00000106803	Chromatin interaction
ENSG00000233246	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv470053	chr4:90879613-91439573	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv879537	chr4:90883047-91165346	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv931074	chr4:90970476-91753697	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830006	chr4:90971656-91186340	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv879538	chr4:90993172-91080308	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv879539	chr4:91015463-91065352	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3357727	chr4:91048154-91050702	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:91047800-91049600	Active TSS	Brain Anterior Caudate	brain
2	chr4:91047800-91049800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:91047800-91051000	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr4:91047800-91051200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:91048000-91048600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:91048000-91048600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr4:91048000-91048600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
8	chr4:91048000-91048800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:91048000-91049000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr4:91048000-91049000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
11	chr4:91048000-91049000	Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr4:91048000-91049000	Flanking Active TSS	HUVEC	blood vessel
13	chr4:91048000-91049200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:91048000-91049200	Active TSS	Brain Germinal Matrix	brain
15	chr4:91048000-91049600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr4:91048000-91049600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr4:91048000-91049600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr4:91048000-91049600	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr4:91048000-91049600	Active TSS	Fetal Brain Male	brain
20	chr4:91048000-91049600	Active TSS	Fetal Kidney	kidney
21	chr4:91048000-91049800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr4:91048000-91049800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:91048000-91049800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:91048000-91049800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr4:91048000-91050000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:91048000-91050000	Active TSS	Stomach Smooth Muscle	stomach
27	chr4:91048000-91050000	Active TSS	NHEK	skin
28	chr4:91048000-91050200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr4:91048000-91050200	Active TSS	Brain Angular Gyrus	brain
30	chr4:91048000-91050400	Active TSS	Brain Hippocampus Middle	brain
31	chr4:91048000-91050600	Active TSS	Brain Cingulate Gyrus	brain
32	chr4:91048000-91050600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:91048000-91050600	Active TSS	Rectal Smooth Muscle	rectum
34	chr4:91048000-91050800	Active TSS	Duodenum Mucosa	Duodenum
35	chr4:91048000-91050800	Active TSS	Fetal Intestine Large	intestine
36	chr4:91048200-91048600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:91048200-91048600	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
38	chr4:91048200-91048600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:91048200-91048600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
40	chr4:91048200-91048600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr4:91048200-91048600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:91048200-91048600	Flanking Active TSS	Placenta	Placenta
43	chr4:91048200-91048600	Flanking Active TSS	Psoas Muscle	Psoas
44	chr4:91048200-91048600	Active TSS	HMEC	breast
45	chr4:91048200-91048600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr4:91048200-91048800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
47	chr4:91048200-91048800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:91048200-91048800	Flanking Active TSS	Colonic Mucosa	Colon
49	chr4:91048200-91049000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr4:91048200-91049000	Bivalent/Poised TSS	Primary T cells from cord blood	blood

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