Variant report

Variant	rs28363906
Chromosome Location	chr4:78978198-78978199
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	POLR2A	chr4:78977771-78978322	SK-N-MC	brain:	n/a	n/a
2	TEAD4	chr4:78977784-78978266	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr4:78977509-78978626	HCT-116	colon:	n/a	chr4:78978542-78978558
4	POLR2A	chr4:78977299-78979342	HCT-116	colon:	n/a	n/a
5	POLR2A	chr4:78977448-78979456	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr4:78977778-78978218	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr4:78978160-78978310	BE2_C	brain:	n/a	chr4:78978165-78978173
8	FOS	chr4:78977970-78978216	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr4:78977385-78979291	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr4:78977281-78978665	H1-hESC	embryonic stem cell:	n/a	chr4:78978115-78978132
11	YY1	chr4:78977826-78978268	SK-N-SH_RA	brain:	n/a	chr4:78978115-78978132
12	HA-E2F1	chr4:78977201-78978378	MCF-7	breast:	n/a	chr4:78977366-78977375
13	POLR2A	chr4:78978163-78978223	ProgFib	skin:	n/a	n/a
14	GTF2F1	chr4:78977922-78978435	H1-hESC	embryonic stem cell:	n/a	n/a
15	CEBPB	chr4:78977208-78978436	H1-hESC	embryonic stem cell:	n/a	n/a
16	MYC	chr4:78977902-78978228	MCF10A-Er-Src	breast:	n/a	chr4:78978075-78978084 chr4:78978074-78978085
17	MBD4	chr4:78977370-78978420	HepG2	liver:	n/a	n/a
18	POLR2A	chr4:78977429-78978219	H1-hESC	embryonic stem cell:	n/a	n/a
19	EP300	chr4:78977401-78978300	HepG2	liver:	n/a	n/a
20	TAF7	chr4:78977408-78979176	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr4:78977462-78978967	H1-hESC	embryonic stem cell:	n/a	n/a
22	RAD21	chr4:78977262-78978280	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr4:78977299-78979313	HCT-116	colon:	n/a	n/a
24	TAF1	chr4:78977841-78978292	PFSK-1	brain:	n/a	n/a
25	YY1	chr4:78977857-78978251	SK-N-SH_RA	brain:	n/a	chr4:78978115-78978132
26	KAP1	chr4:78977418-78978754	HEK293	kidney:	n/a	n/a
27	ZBTB7A	chr4:78977550-78978873	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr4:78977387-78978569	ECC-1	luminal epithelium:	n/a	n/a
29	MXI1	chr4:78977253-78979420	HepG2	liver:	n/a	chr4:78978076-78978085
30	REST	chr4:78977801-78978256	A549	lung:	n/a	n/a
31	YY1	chr4:78977858-78978264	HCT-116	colon:	n/a	chr4:78978115-78978132
32	ZBTB7A	chr4:78977436-78978765	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr4:78977348-78981234	SK-N-SH	brain:	n/a	chr4:78979876-78979886 chr4:78980842-78980855 chr4:78978165-78978173 chr4:78980844-78980854
34	POLR2A	chr4:78978068-78978254	HepG2	liver:	n/a	n/a
35	TBP	chr4:78977898-78978370	Hela-S3	cervix:	n/a	n/a
36	MXI1	chr4:78977811-78978210	GM12878	blood:	n/a	chr4:78978076-78978085
37	ELF1	chr4:78977450-78978232	HepG2	liver:	n/a	n/a
38	YY1	chr4:78977338-78978899	HepG2	liver:	n/a	chr4:78978115-78978132
39	MXI1	chr4:78977162-78978576	H1-hESC	embryonic stem cell:	n/a	chr4:78978076-78978085
40	POLR2A	chr4:78977167-78979826	HepG2	liver:	n/a	n/a
41	USF1	chr4:78977789-78978299	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:78977637-78978369	ECC-1	luminal epithelium:	n/a	n/a
43	SIN3AK20	chr4:78977397-78979631	MCF-7	breast:	n/a	n/a
44	FOXA2	chr4:78977720-78978219	HepG2	liver:	n/a	n/a
45	HDAC2	chr4:78977394-78978271	HepG2	liver:	n/a	n/a
46	POLR2A	chr4:78977833-78978317	HepG2	liver:	n/a	n/a
47	ARID3A	chr4:78977230-78978408	HepG2	liver:	n/a	chr4:78978120-78978135
48	USF1	chr4:78977886-78978336	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr4:78977891-78978810	Hela-S3	cervix:	n/a	n/a
50	BACH1	chr4:78977265-78978275	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:78977205..78980008-chr4:79470660..79474757,5	MCF-7	breast:
2	chr4:78975304..78979082-chr4:79472141..79474367,3	MCF-7	breast:
3	chr4:78925853..78927440-chr4:78976402..78978682,2	MCF-7	breast:
4	chr4:78739575..78742806-chr4:78977392..78979889,3	MCF-7	breast:

Variant related genes	Relation type
FRAS1	TF binding region
ENSG00000138767	Chromatin interaction
ENSG00000138772	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10461184	0.95[ASN][1000 genomes]
rs13129248	0.85[ASN][1000 genomes]
rs28398889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28500721	0.98[ASN][1000 genomes]
rs36045725	0.85[ASN][1000 genomes]
rs6832285	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription 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	14 gene(s)	inside rSNPs	diseases
6	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS 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	14 gene(s)	inside rSNPs	diseases
7	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
9	nsv4396	chr4:78935347-78980705	Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr4:78977000-78979000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr4:78977000-78979200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr4:78977000-78980800	Active TSS	Left Ventricle	heart
4	chr4:78977000-78981200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:78977200-78978200	Active TSS	Brain Germinal Matrix	brain
6	chr4:78977200-78978200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
7	chr4:78977200-78978400	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr4:78977200-78978600	Flanking Active TSS	HMEC	breast
9	chr4:78977200-78978600	Flanking Active TSS	NH-A	brain
10	chr4:78977200-78978800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr4:78977200-78979000	Active TSS	Fetal Brain Male	brain
12	chr4:78977200-78979000	Active TSS	Fetal Brain Female	brain
13	chr4:78977200-78979200	Active TSS	Rectal Smooth Muscle	rectum
14	chr4:78977200-78980800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr4:78977200-78980800	Active TSS	Psoas Muscle	Psoas
16	chr4:78977200-78981000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:78977200-78981000	Active TSS	Brain Angular Gyrus	brain
18	chr4:78977200-78981000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:78977200-78981000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr4:78977200-78981000	Active TSS	Right Ventricle	heart
21	chr4:78977200-78981000	Active TSS	A549	lung
22	chr4:78977200-78981200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:78977200-78981400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr4:78977400-78978200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
25	chr4:78977400-78978200	Flanking Active TSS	Spleen	Spleen
26	chr4:78977400-78978400	Flanking Active TSS	Esophagus	oesophagus
27	chr4:78977400-78978400	Flanking Active TSS	Placenta	Placenta
28	chr4:78977400-78978400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
29	chr4:78977400-78978600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr4:78977400-78979200	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr4:78977400-78979200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:78977400-78979400	Active TSS	Colon Smooth Muscle	Colon
33	chr4:78977400-78979800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr4:78977400-78980200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr4:78977400-78980800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:78977400-78980800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:78977400-78980800	Active TSS	Aorta	Aorta
38	chr4:78977400-78980800	Active TSS	Fetal Heart	heart
39	chr4:78977400-78980800	Active TSS	Hela-S3	cervix
40	chr4:78977400-78981000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr4:78977400-78981000	Active TSS	HSMMtube	muscle
42	chr4:78977400-78981600	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr4:78977400-78982000	Active TSS	H1 Cell Line	embryonic stem cell
44	chr4:78977600-78978200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:78977600-78978400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
46	chr4:78977600-78978400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:78977600-78978400	Flanking Bivalent TSS/Enh	Dnd41	blood
48	chr4:78977600-78978600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
49	chr4:78977600-78978800	Flanking Bivalent TSS/Enh	Osteobl	bone
50	chr4:78977600-78979600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum

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