Variant report

Variant	rs28398889
Chromosome Location	chr4:78978673-78978674
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	chr4:78977299-78979342	HCT-116	colon:	n/a	n/a
2	POLR2A	chr4:78977448-78979456	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr4:78978351-78978843	ProgFib	skin:	n/a	n/a
4	POLR2A	chr4:78977385-78979291	H1-hESC	embryonic stem cell:	n/a	n/a
5	TAF7	chr4:78977408-78979176	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:78977462-78978967	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr4:78977299-78979313	HCT-116	colon:	n/a	n/a
8	KAP1	chr4:78977418-78978754	HEK293	kidney:	n/a	n/a
9	ZBTB7A	chr4:78977550-78978873	ECC-1	luminal epithelium:	n/a	n/a
10	MXI1	chr4:78977253-78979420	HepG2	liver:	n/a	chr4:78978076-78978085
11	ZBTB7A	chr4:78977436-78978765	ECC-1	luminal epithelium:	n/a	n/a
12	CTCF	chr4:78977348-78981234	SK-N-SH	brain:	n/a	chr4:78979876-78979886 chr4:78980842-78980855 chr4:78978165-78978173 chr4:78980844-78980854
13	CHD2	chr4:78978463-78978991	HepG2	liver:	n/a	n/a
14	YY1	chr4:78977338-78978899	HepG2	liver:	n/a	chr4:78978115-78978132
15	POLR2A	chr4:78977167-78979826	HepG2	liver:	n/a	n/a
16	SIN3AK20	chr4:78977397-78979631	MCF-7	breast:	n/a	n/a
17	CREB1	chr4:78978413-78978937	A549	lung:	n/a	n/a
18	POLR2A	chr4:78977891-78978810	Hela-S3	cervix:	n/a	n/a
19	HEY1	chr4:78977470-78978987	HepG2	liver:	n/a	chr4:78977517-78977532
20	POLR2A	chr4:78978394-78978894	HepG2	liver:	n/a	n/a
21	JUND	chr4:78977289-78978827	H1-hESC	embryonic stem cell:	n/a	chr4:78977368-78977377
22	POLR2A	chr4:78977469-78979010	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr4:78977224-78980926	HepG2	liver:	n/a	n/a
24	TCF7L2	chr4:78977068-78979740	HCT-116	colon:	n/a	chr4:78977818-78977834 chr4:78977822-78977832 chr4:78977822-78977831 chr4:78977818-78977834 chr4:78977821-78977830
25	NFIC	chr4:78977504-78979398	ECC-1	luminal epithelium:	n/a	chr4:78978380-78978408
26	RAD21	chr4:78977403-78978796	HepG2	liver:	n/a	n/a
27	POLR2A	chr4:78978403-78978695	A549	lung:	n/a	n/a
28	MAX	chr4:78977205-78978829	HepG2	liver:	n/a	chr4:78978075-78978084 chr4:78978074-78978085 chr4:78977394-78977403
29	TAF1	chr4:78978503-78978925	A549	lung:	n/a	n/a
30	POLR2A	chr4:78978353-78978982	HepG2	liver:	n/a	n/a
31	CEBPD	chr4:78978245-78978758	HepG2	liver:	n/a	n/a
32	SMC3	chr4:78977082-78981444	SK-N-SH	brain:	n/a	chr4:78980845-78980855 chr4:78979878-78979886 chr4:78979875-78979885 chr4:78980841-78980855
33	POLR2A	chr4:78977060-78980991	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr4:78977452-78979410	HepG2	liver:	n/a	n/a
35	TAF1	chr4:78978539-78978913	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr4:78977215-78979413	MCF-7	breast:	n/a	n/a
37	MYBL2	chr4:78977459-78978699	HepG2	liver:	n/a	n/a
38	RAD21	chr4:78977189-78981892	SK-N-SH	brain:	n/a	chr4:78980840-78980859 chr4:78980845-78980855 chr4:78980843-78980856 chr4:78980720-78980733
39	MAX	chr4:78977517-78980318	ECC-1	luminal epithelium:	n/a	chr4:78978075-78978084 chr4:78978074-78978085
40	TCF7L2	chr4:78977600-78978676	Hela-S3	cervix:	n/a	chr4:78977818-78977834 chr4:78977822-78977832 chr4:78977822-78977831 chr4:78977818-78977834 chr4:78977821-78977830
41	POLR2A	chr4:78977414-78978978	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:78977519-78978939	HCT-116	colon:	n/a	n/a
43	MAX	chr4:78977440-78978843	SK-N-SH	brain:	n/a	chr4:78978075-78978084 chr4:78978074-78978085
44	NFIC	chr4:78977400-78979582	SK-N-SH	brain:	n/a	chr4:78978380-78978408
45	MAX	chr4:78977279-78979530	HepG2	liver:	n/a	chr4:78978075-78978084 chr4:78978074-78978085 chr4:78977394-78977403
46	TAF1	chr4:78978272-78978723	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr4:78978238-78978753	H1-neurons	neurons:	n/a	n/a
48	POLR2A	chr4:78978663-78978731	MCF10A-Er-Src	breast:	n/a	n/a
49	SIN3A	chr4:78976988-78981317	H1-hESC	embryonic stem cell:	n/a	chr4:78980508-78980517 chr4:78980166-78980175 chr4:78978544-78978555 chr4:78978076-78978085
50	BHLHE40	chr4:78977275-78978783	HepG2	liver:	n/a	chr4:78978542-78978558

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	0.97[ASN][1000 genomes]
rs13129248	0.87[ASN][1000 genomes]
rs28363906	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	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs36045725	0.87[ASN][1000 genomes]
rs6832285	0.85[AFR][1000 genomes];1.00[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:124 , 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	chr4:78977200-78978800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
6	chr4:78977200-78979000	Active TSS	Fetal Brain Male	brain
7	chr4:78977200-78979000	Active TSS	Fetal Brain Female	brain
8	chr4:78977200-78979200	Active TSS	Rectal Smooth Muscle	rectum
9	chr4:78977200-78980800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr4:78977200-78980800	Active TSS	Psoas Muscle	Psoas
11	chr4:78977200-78981000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:78977200-78981000	Active TSS	Brain Angular Gyrus	brain
13	chr4:78977200-78981000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:78977200-78981000	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr4:78977200-78981000	Active TSS	Right Ventricle	heart
16	chr4:78977200-78981000	Active TSS	A549	lung
17	chr4:78977200-78981200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:78977200-78981400	Active TSS	H9 Cell Line	embryonic stem cell
19	chr4:78977400-78979200	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr4:78977400-78979200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:78977400-78979400	Active TSS	Colon Smooth Muscle	Colon
22	chr4:78977400-78979800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
23	chr4:78977400-78980200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr4:78977400-78980800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:78977400-78980800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:78977400-78980800	Active TSS	Aorta	Aorta
27	chr4:78977400-78980800	Active TSS	Fetal Heart	heart
28	chr4:78977400-78980800	Active TSS	Hela-S3	cervix
29	chr4:78977400-78981000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:78977400-78981000	Active TSS	HSMMtube	muscle
31	chr4:78977400-78981600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr4:78977400-78982000	Active TSS	H1 Cell Line	embryonic stem cell
33	chr4:78977600-78978800	Flanking Bivalent TSS/Enh	Osteobl	bone
34	chr4:78977600-78979600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
35	chr4:78977600-78979800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
36	chr4:78977600-78980000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:78977600-78980000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:78977600-78980200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
39	chr4:78977600-78980200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
40	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
41	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
42	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr4:78977600-78980600	Active TSS	Gastric	stomach
44	chr4:78977600-78980600	Bivalent/Poised TSS	HepG2	liver
45	chr4:78977600-78980600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr4:78977600-78980800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:78977600-78980800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
48	chr4:78977600-78981000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:78977600-78981000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr4:78977600-78981000	Active TSS	Fetal Intestine Large	intestine

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