Variant report

Variant	rs28489758
Chromosome Location	chr4:128620358-128620359
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	FOSL2	chr4:128619819-128620424	SK-N-SH	brain:	n/a	n/a
2	CUX1	chr4:128619681-128620360	GM12878	blood:	n/a	n/a
3	BATF	chr4:128619916-128620358	GM12878	blood:	n/a	n/a
4	PML	chr4:128619841-128620359	GM12878	blood:	n/a	n/a
5	RAD21	chr4:128620031-128620372	Hela-S3	cervix:	n/a	n/a
6	FOXM1	chr4:128619713-128620366	GM12878	blood:	n/a	n/a
7	JUND	chr4:128619781-128620448	HCT-116	colon:	n/a	n/a
8	ATF3	chr4:128619938-128620425	HCT-116	colon:	n/a	n/a
9	RCOR1	chr4:128619937-128620537	GM12878	blood:	n/a	n/a
10	SP1	chr4:128619775-128620592	HCT-116	colon:	n/a	n/a
11	FOS	chr4:128619917-128620359	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr4:128619917-128620548	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF12	chr4:128619824-128620478	SK-N-SH	brain:	n/a	n/a
14	JUND	chr4:128619968-128620857	Hela-S3	cervix:	n/a	chr4:128620775-128620784
15	PBX3	chr4:128619934-128620406	SK-N-SH	brain:	n/a	n/a
16	SP1	chr4:128619813-128620376	HCT-116	colon:	n/a	n/a
17	RAD21	chr4:128619919-128620363	HCT-116	colon:	n/a	n/a
18	RUNX3	chr4:128619661-128620378	GM12878	blood:	n/a	n/a
19	TCF7L2	chr4:128620045-128620408	Hela-S3	cervix:	n/a	n/a
20	SRF	chr4:128619797-128620425	HCT-116	colon:	n/a	n/a
21	GATA3	chr4:128619918-128620503	SK-N-SH	brain:	n/a	n/a
22	JUND	chr4:128619896-128620441	SK-N-SH	brain:	n/a	n/a
23	MYC	chr4:128620028-128620397	MCF10A-Er-Src	breast:	n/a	n/a
24	FOSL2	chr4:128619904-128620365	A549	lung:	n/a	n/a
25	TEAD4	chr4:128619888-128620422	HCT-116	colon:	n/a	n/a
26	CBX3	chr4:128619911-128620372	HCT-116	colon:	n/a	n/a
27	STAT3	chr4:128620062-128620366	Hela-S3	cervix:	n/a	n/a
28	RCOR1	chr4:128620014-128620639	Hela-S3	cervix:	n/a	n/a
29	EP300	chr4:128619921-128620413	ECC-1	luminal epithelium:	n/a	chr4:128620152-128620166
30	JUND	chr4:128619800-128620436	HCT-116	colon:	n/a	n/a
31	SIN3AK20	chr4:128619934-128620457	HCT-116	colon:	n/a	n/a
32	CEBPB	chr4:128620047-128620457	ECC-1	luminal epithelium:	n/a	chr4:128620151-128620164
33	NFIC	chr4:128619853-128620516	ECC-1	luminal epithelium:	n/a	n/a
34	SIN3AK20	chr4:128619895-128620422	HCT-116	colon:	n/a	n/a
35	CEBPB	chr4:128620085-128620432	A549	lung:	n/a	chr4:128620151-128620164
36	POLR2A	chr4:128620248-128620374	MCF10A-Er-Src	breast:	n/a	n/a
37	TEAD4	chr4:128619916-128620469	ECC-1	luminal epithelium:	n/a	n/a
38	MAX	chr4:128620070-128620372	Hela-S3	cervix:	n/a	n/a
39	MAX	chr4:128620102-128620389	SK-N-SH	brain:	n/a	n/a
40	FOSL1	chr4:128619829-128620429	HCT-116	colon:	n/a	n/a
41	ZNF384	chr4:128619576-128620428	GM12878	blood:	n/a	chr4:128619730-128619738
42	RAD21	chr4:128619994-128620363	ECC-1	luminal epithelium:	n/a	n/a
43	FOSL1	chr4:128619810-128620481	HCT-116	colon:	n/a	n/a
44	STAT3	chr4:128619909-128620373	MCF10A-Er-Src	breast:	n/a	n/a
45	TEAD4	chr4:128619960-128620397	ECC-1	luminal epithelium:	n/a	n/a
46	CBX3	chr4:128619927-128620413	HCT-116	colon:	n/a	n/a
47	CREB1	chr4:128619888-128620393	GM12878	blood:	n/a	n/a
48	FOS	chr4:128619940-128620388	MCF10A-Er-Src	breast:	n/a	n/a
49	CEBPB	chr4:128619883-128620426	GM12878	blood:	n/a	chr4:128620151-128620164
50	EP300	chr4:128619853-128620360	GM12878	blood:	n/a	chr4:128620152-128620166

Variant related genes	Relation type
INTU	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10009032	1.00[MEX][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs10011964	0.91[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs10014097	0.92[AFR][1000 genomes]
rs10022669	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023183	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023194	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10024724	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10026828	1.00[AMR][1000 genomes]
rs10027661	0.91[AFR][1000 genomes]
rs10032340	0.81[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10034548	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10034679	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11934062	1.00[MEX][hapmap]
rs13434829	1.00[AMR][1000 genomes]
rs17012567	0.84[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17012568	0.92[ASW][hapmap];1.00[MEX][hapmap]
rs1913465	1.00[AMR][1000 genomes]
rs28436595	0.91[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs28655300	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28742883	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28765108	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28786410	1.00[AMR][1000 genomes]
rs28791046	1.00[AMR][1000 genomes]
rs4324559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4550948	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9992298	0.91[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv879920	chr4:128554404-128694288	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv879921	chr4:128554404-128766074	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv879924	chr4:128566686-128622430	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	esv1793579	chr4:128577439-128871309	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
19	esv1792152	chr4:128585215-128752829	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv879925	chr4:128586241-128665981	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv830057	chr4:128591288-128788777	Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128554600-128627400	Weak transcription	Pancreas	Pancrea
2	chr4:128554600-128644800	Weak transcription	Lung	lung
3	chr4:128555600-128627600	Weak transcription	Brain Angular Gyrus	brain
4	chr4:128563600-128627400	Weak transcription	Brain Substantia Nigra	brain
5	chr4:128566600-128644600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:128597000-128630200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:128597000-128651600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:128597600-128632000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:128597600-128632000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:128597800-128627600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:128598200-128627400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:128598200-128638200	Weak transcription	Esophagus	oesophagus
13	chr4:128604400-128634400	Weak transcription	Fetal Heart	heart
14	chr4:128606200-128627400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:128606200-128638200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:128607000-128627400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:128607600-128627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:128607800-128627400	Weak transcription	Left Ventricle	heart
19	chr4:128608400-128630200	Weak transcription	Gastric	stomach
20	chr4:128608400-128643800	Weak transcription	Right Ventricle	heart
21	chr4:128609200-128627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:128609800-128636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr4:128611200-128627800	Weak transcription	Fetal Stomach	stomach
24	chr4:128612200-128632200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:128612800-128626600	Weak transcription	Adipose Nuclei	Adipose
26	chr4:128614800-128627600	Weak transcription	HSMMtube	muscle
27	chr4:128615200-128642000	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:128615200-128648800	Weak transcription	Fetal Kidney	kidney
29	chr4:128615400-128630200	Weak transcription	Brain Germinal Matrix	brain
30	chr4:128616200-128626600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:128616200-128627800	Weak transcription	Fetal Lung	lung
32	chr4:128616200-128646200	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:128616400-128625400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:128616400-128627400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:128616400-128627400	Weak transcription	Fetal Brain Female	brain
36	chr4:128616400-128627400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:128616600-128627400	Weak transcription	Aorta	Aorta
38	chr4:128616800-128626400	Weak transcription	Ovary	ovary
39	chr4:128617000-128627400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:128617000-128643400	Weak transcription	Fetal Intestine Small	intestine
41	chr4:128617200-128635600	Weak transcription	Fetal Brain Male	brain
42	chr4:128618800-128626400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:128619000-128631600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:128619400-128620400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:128619400-128620400	Enhancers	GM12878-XiMat	blood
46	chr4:128619600-128620400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr4:128619600-128620600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:128619600-128620600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr4:128619600-128620600	Enhancers	NH-A	brain
50	chr4:128619600-128620800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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