Variant report

Variant	rs28500721
Chromosome Location	chr4:78978431-78978432
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	USF1	chr4:78977509-78978626	HCT-116	colon:	n/a	chr4:78978542-78978558
2	POLR2A	chr4:78977299-78979342	HCT-116	colon:	n/a	n/a
3	CTCF	chr4:78978359-78978534	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr4:78978427-78978657	A549	lung:	n/a	n/a
5	CTCF	chr4:78978400-78978550	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:78977448-78979456	H1-neurons	neurons:	n/a	n/a
7	CTCF	chr4:78978300-78978450	BE2_C	brain:	n/a	n/a
8	POLR2A	chr4:78978351-78978843	ProgFib	skin:	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	SMC3	chr4:78978369-78978523	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr4:78978321-78978564	GM12878	blood:	n/a	n/a
13	GTF2F1	chr4:78977922-78978435	H1-hESC	embryonic stem cell:	n/a	n/a
14	CEBPB	chr4:78977208-78978436	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr4:78978400-78978550	HUVEC	blood vessel:	n/a	n/a
16	CTCF	chr4:78978400-78978550	SK-N-SH_RA	brain:	n/a	n/a
17	TAF7	chr4:78977408-78979176	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:78977462-78978967	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F4	chr4:78978429-78978457	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr4:78978420-78978570	HRE	kidney:	n/a	n/a
21	CTCF	chr4:78978350-78978560	NHEK	skin:	n/a	n/a
22	CTCF	chr4:78978320-78978470	GM12867	blood:	n/a	n/a
23	CTCF	chr4:78978380-78978530	HFF	foreskin:	n/a	n/a
24	POLR2A	chr4:78977299-78979313	HCT-116	colon:	n/a	n/a
25	KAP1	chr4:78977418-78978754	HEK293	kidney:	n/a	n/a
26	ZBTB7A	chr4:78977550-78978873	ECC-1	luminal epithelium:	n/a	n/a
27	TAF1	chr4:78977387-78978569	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr4:78978400-78978550	HCPEpiC	choroid plexus:	n/a	n/a
29	MXI1	chr4:78977253-78979420	HepG2	liver:	n/a	chr4:78978076-78978085
30	ZBTB7A	chr4:78977436-78978765	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr4:78977348-78981234	SK-N-SH	brain:	n/a	chr4:78979876-78979886 chr4:78980842-78980855 chr4:78978165-78978173 chr4:78980844-78980854
32	CTCF	chr4:78978380-78978530	Caco-2	colon:	n/a	n/a
33	YY1	chr4:78977338-78978899	HepG2	liver:	n/a	chr4:78978115-78978132
34	MXI1	chr4:78977162-78978576	H1-hESC	embryonic stem cell:	n/a	chr4:78978076-78978085
35	POLR2A	chr4:78977167-78979826	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr4:78977397-78979631	MCF-7	breast:	n/a	n/a
37	CREB1	chr4:78978413-78978937	A549	lung:	n/a	n/a
38	POLR2A	chr4:78977891-78978810	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr4:78978396-78978583	Hela-S3	cervix:	n/a	n/a
40	HEY1	chr4:78977470-78978987	HepG2	liver:	n/a	chr4:78977517-78977532
41	POLR2A	chr4:78978394-78978894	HepG2	liver:	n/a	n/a
42	MYC	chr4:78978425-78978554	HepG2	liver:	n/a	n/a
43	CTCF	chr4:78978393-78978562	ProgFib	skin:	n/a	n/a
44	JUND	chr4:78977289-78978827	H1-hESC	embryonic stem cell:	n/a	chr4:78977368-78977377
45	CTCF	chr4:78978380-78978530	HEK293	kidney:	n/a	n/a
46	MAZ	chr4:78977510-78978494	HepG2	liver:	n/a	chr4:78978075-78978084 chr4:78978074-78978085
47	POLR2A	chr4:78977469-78979010	ECC-1	luminal epithelium:	n/a	n/a
48	USF1	chr4:78977325-78978655	HCT-116	colon:	n/a	chr4:78978542-78978558
49	YY1	chr4:78977758-78978478	ECC-1	luminal epithelium:	n/a	chr4:78978115-78978132
50	CTCF	chr4:78978400-78978550	AG04449	skin:	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	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13129248	0.87[ASN][1000 genomes]
rs28363906	0.98[ASN][1000 genomes]
rs28398889	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36045725	0.87[ASN][1000 genomes]
rs6832285	0.83[AMR][1000 genomes];1.00[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:126 , 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	chr4:78977200-78978600	Flanking Active TSS	HMEC	breast
6	chr4:78977200-78978600	Flanking Active TSS	NH-A	brain
7	chr4:78977200-78978800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
8	chr4:78977200-78979000	Active TSS	Fetal Brain Male	brain
9	chr4:78977200-78979000	Active TSS	Fetal Brain Female	brain
10	chr4:78977200-78979200	Active TSS	Rectal Smooth Muscle	rectum
11	chr4:78977200-78980800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr4:78977200-78980800	Active TSS	Psoas Muscle	Psoas
13	chr4:78977200-78981000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:78977200-78981000	Active TSS	Brain Angular Gyrus	brain
15	chr4:78977200-78981000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:78977200-78981000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr4:78977200-78981000	Active TSS	Right Ventricle	heart
18	chr4:78977200-78981000	Active TSS	A549	lung
19	chr4:78977200-78981200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:78977200-78981400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr4:78977400-78978600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr4:78977400-78979200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:78977400-78979200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:78977400-78979400	Active TSS	Colon Smooth Muscle	Colon
25	chr4:78977400-78979800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr4:78977400-78980200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr4:78977400-78980800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:78977400-78980800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:78977400-78980800	Active TSS	Aorta	Aorta
30	chr4:78977400-78980800	Active TSS	Fetal Heart	heart
31	chr4:78977400-78980800	Active TSS	Hela-S3	cervix
32	chr4:78977400-78981000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:78977400-78981000	Active TSS	HSMMtube	muscle
34	chr4:78977400-78981600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr4:78977400-78982000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr4:78977600-78978600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
37	chr4:78977600-78978800	Flanking Bivalent TSS/Enh	Osteobl	bone
38	chr4:78977600-78979600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
39	chr4:78977600-78979800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
40	chr4:78977600-78980000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:78977600-78980000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:78977600-78980200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
43	chr4:78977600-78980200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
44	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
45	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
47	chr4:78977600-78980600	Active TSS	Gastric	stomach
48	chr4:78977600-78980600	Bivalent/Poised TSS	HepG2	liver
49	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
50	chr4:78977600-78980800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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