Variant report

Variant	rs1441908
Chromosome Location	chr4:77172595-77172596
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	SIN3A	chr4:77172539-77173394	H1-hESC	embryonic stem cell:	n/a	chr4:77172983-77172992 chr4:77172716-77172729
2	POLR2A	chr4:77172426-77173313	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr4:77172080-77173216	ECC-1	luminal epithelium:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
4	MAX	chr4:77172169-77173246	MCF-7	breast:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
5	POLR2A	chr4:77172573-77173112	MCF10A-Er-Src	breast:	n/a	n/a
6	GTF2F1	chr4:77172292-77172904	H1-hESC	embryonic stem cell:	n/a	n/a
7	E2F6	chr4:77172119-77173190	H1-hESC	embryonic stem cell:	n/a	chr4:77172784-77172794 chr4:77172837-77172847
8	EP300	chr4:77172564-77173107	H1-hESC	embryonic stem cell:	n/a	n/a
9	SMC3	chr4:77172581-77173238	HepG2	liver:	n/a	n/a
10	MAX	chr4:77172478-77173150	SK-N-SH	brain:	n/a	n/a
11	BHLHE40	chr4:77172572-77173142	HepG2	liver:	n/a	n/a
12	HDAC2	chr4:77172542-77173158	H1-hESC	embryonic stem cell:	n/a	chr4:77172566-77172580
13	MAX	chr4:77171995-77173182	H1-hESC	embryonic stem cell:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
14	MAX	chr4:77172132-77173139	MCF-7	breast:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
15	MAZ	chr4:77172587-77173245	HepG2	liver:	n/a	n/a
16	MAX	chr4:77172121-77173242	ECC-1	luminal epithelium:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
17	MAX	chr4:77172526-77173134	A549	lung:	n/a	n/a
18	POLR2A	chr4:77172231-77173284	H1-hESC	embryonic stem cell:	n/a	n/a
19	RFX5	chr4:77172516-77173056	HepG2	liver:	n/a	chr4:77172778-77172794 chr4:77172825-77172839 chr4:77172823-77172837 chr4:77172827-77172836 chr4:77172780-77172789
20	TEAD4	chr4:77172558-77173039	ECC-1	luminal epithelium:	n/a	n/a
21	MAX	chr4:77172479-77173069	K562	blood:	n/a	n/a
22	MAX	chr4:77172258-77173117	HepG2	liver:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
23	POLR2A	chr4:77172563-77173303	MCF-7	breast:	n/a	n/a
24	USF2	chr4:77172197-77172676	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF143	chr4:77172475-77173424	H1-hESC	embryonic stem cell:	n/a	chr4:77173184-77173202
26	YY1	chr4:77172536-77173497	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
27	MAX	chr4:77172066-77173262	HepG2	liver:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
28	SIN3AK20	chr4:77172577-77173045	PANC-1	pancreas:	n/a	n/a
29	E2F6	chr4:77171918-77173496	H1-hESC	embryonic stem cell:	n/a	chr4:77172784-77172794 chr4:77172837-77172847 chr4:77173336-77173346 chr4:77173185-77173194
30	RFX5	chr4:77171988-77173158	IMR90	lung:	n/a	chr4:77172778-77172794 chr4:77172825-77172839 chr4:77172823-77172837 chr4:77172827-77172836 chr4:77172780-77172789
31	POLR2A	chr4:77172536-77173009	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr4:77172584-77173329	MCF-7	breast:	n/a	n/a
33	MYC	chr4:77172549-77173030	MCF10A-Er-Src	breast:	n/a	n/a
34	MAX	chr4:77172118-77173018	H1-hESC	embryonic stem cell:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
35	REST	chr4:77172293-77173256	H1-neurons	neurons:	n/a	chr4:77172340-77172358 chr4:77172716-77172729 chr4:77172983-77172993
36	MAX	chr4:77172142-77173145	H1-hESC	embryonic stem cell:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294
37	POLR2A	chr4:77172466-77173074	H1-neurons	neurons:	n/a	n/a
38	E2F6	chr4:77172589-77173088	K562	blood:	n/a	chr4:77172784-77172794 chr4:77172837-77172847
39	E2F6	chr4:77172404-77172988	A549	lung:	n/a	chr4:77172784-77172794 chr4:77172837-77172847
40	GATA2	chr4:77172305-77173537	SH-SY5Y	brain:	n/a	n/a
41	POLR2A	chr4:77172522-77173159	H1-neurons	neurons:	n/a	n/a
42	HA-E2F1	chr4:77172336-77173270	MCF-7	breast:	n/a	chr4:77172784-77172794 chr4:77172837-77172847 chr4:77173185-77173194
43	MAX	chr4:77172466-77173169	SK-N-SH	brain:	n/a	n/a
44	MXI1	chr4:77172595-77173191	HepG2	liver:	n/a	n/a
45	POLR2A	chr4:77172571-77173106	MCF-7	breast:	n/a	n/a
46	SIN3AK20	chr4:77172141-77173631	MCF-7	breast:	n/a	n/a
47	YY1	chr4:77172570-77173491	H1-hESC	embryonic stem cell:	n/a	chr4:77173390-77173409 chr4:77173051-77173060 chr4:77173398-77173406 chr4:77173049-77173060
48	RFX5	chr4:77171716-77173784	SK-N-SH	brain:	n/a	chr4:77172778-77172794 chr4:77172825-77172839 chr4:77172823-77172837 chr4:77172827-77172836 chr4:77172780-77172789
49	MYC	chr4:77172201-77172740	H1-hESC	embryonic stem cell:	n/a	chr4:77172282-77172295 chr4:77172284-77172294 chr4:77172284-77172293 chr4:77172285-77172292 chr4:77172283-77172293 chr4:77172284-77172293 chr4:77172283-77172294

No.	Distal block	Cell Line	Cell type
1	chr4:77069302..77071113-chr4:77170408..77173032,2	MCF-7	breast:
2	chr4:77133278..77135557-chr4:77171656..77174471,3	MCF-7	breast:
3	chr4:77171208..77175531-chr4:77176138..77180024,6	K562	blood:
4	chr4:77171768..77173922-chr4:77226650..77228948,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCARB2-1	chr4:77172297-77172990	NONHSAT096992

Variant related genes	Relation type
ENSG00000272414	TF binding region
FAM47E	TF binding region
FAM47E-STBD1	TF binding region
ENSG00000189157	Chromatin interaction
ENSG00000138760	Chromatin interaction
ENSG00000118804	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10446680	0.90[ASN][1000 genomes]
rs11097296	0.86[ASN][1000 genomes]
rs11097297	0.87[ASN][1000 genomes]
rs11737624	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12331583	0.86[ASN][1000 genomes]
rs12501795	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348206	0.90[ASN][1000 genomes]
rs1348208	0.90[ASN][1000 genomes]
rs1372408	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441906	0.90[ASN][1000 genomes]
rs1441907	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441917	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441918	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441919	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441921	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441922	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197102	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2218264	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28530675	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28718095	0.87[ASN][1000 genomes]
rs2904215	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2904216	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35177915	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35851125	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3919711	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859645	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859647	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56371028	0.89[ASN][1000 genomes]
rs6814385	0.86[ASN][1000 genomes]
rs6837231	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6837841	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6854218	0.86[ASN][1000 genomes]
rs6855568	0.86[ASN][1000 genomes]
rs7657929	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760851	chr4:77164549-77185144	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv516357	chr4:77167242-77178379	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2421530	chr4:77167242-77178676	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77171600-77173800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr4:77172000-77172600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
3	chr4:77172000-77172600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
4	chr4:77172000-77172600	Bivalent/Poised TSS	Fetal Stomach	stomach
5	chr4:77172000-77172600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
6	chr4:77172000-77172600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:77172000-77173000	Active TSS	Psoas Muscle	Psoas
8	chr4:77172000-77173400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr4:77172000-77173600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:77172000-77173600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr4:77172200-77172600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:77172200-77172600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:77172200-77172600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr4:77172200-77172600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr4:77172200-77172600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:77172200-77172600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:77172200-77172600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
20	chr4:77172200-77172600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:77172200-77172600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
25	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:77172200-77172600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:77172200-77172600	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr4:77172200-77172600	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr4:77172200-77172600	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr4:77172200-77172600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr4:77172200-77172600	Enhancers	Esophagus	oesophagus
33	chr4:77172200-77172600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
35	chr4:77172200-77172600	Flanking Active TSS	Fetal Heart	heart
36	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
37	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
38	chr4:77172200-77172600	Bivalent Enhancer	Fetal Thymus	thymus
39	chr4:77172200-77172600	Enhancers	Lung	lung
40	chr4:77172200-77172600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr4:77172200-77172600	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
43	chr4:77172200-77172600	Flanking Bivalent TSS/Enh	Osteobl	bone
44	chr4:77172200-77172800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:77172200-77172800	Flanking Active TSS	Placenta	Placenta
46	chr4:77172200-77172800	Flanking Bivalent TSS/Enh	HepG2	liver
47	chr4:77172200-77172800	Flanking Bivalent TSS/Enh	HMEC	breast
48	chr4:77172200-77173000	Active TSS	Pancreas	Pancrea
49	chr4:77172200-77173000	Bivalent/Poised TSS	A549	lung
50	chr4:77172200-77173200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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