Variant report

Variant	rs16892028
Chromosome Location	chr4:15480673-15480674
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	RAD21	chr4:15480498-15481267	MCF-7	breast:	n/a	chr4:15480761-15480780
2	CTCF	chr4:15480671-15480869	SK-N-SH_RA	brain:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
3	MYC	chr4:15480641-15481472	K562	blood:	n/a	chr4:15481265-15481274 chr4:15481264-15481275 chr4:15481265-15481274 chr4:15481263-15481276 chr4:15481265-15481275 chr4:15481264-15481274 chr4:15481261-15481276 chr4:15481264-15481275 chr4:15481265-15481274
4	RAD21	chr4:15480462-15481736	HCT-116	colon:	n/a	chr4:15480761-15480780
5	CTCF	chr4:15480663-15480969	K562	blood:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
6	POLR2A	chr4:15480669-15481634	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr4:15480562-15481600	U87	brain:	n/a	n/a
8	SMC3	chr4:15480340-15482176	SK-N-SH	brain:	n/a	chr4:15480762-15480776
9	CTCF	chr4:15480660-15480810	HVMF	connective:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
10	SMC3	chr4:15480467-15481020	GM12878	blood:	n/a	chr4:15480762-15480776
11	CTCF	chr4:15480660-15480810	GM12866	blood:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
12	RAD21	chr4:15480569-15481138	A549	lung:	n/a	chr4:15480761-15480780
13	RAD21	chr4:15480546-15481148	SK-N-SH_RA	brain:	n/a	chr4:15480761-15480780
14	BHLHE40	chr4:15480636-15481445	HepG2	liver:	n/a	chr4:15481086-15481095 chr4:15481085-15481094 chr4:15481084-15481097
15	CTCF	chr4:15480600-15480750	GM12870	blood:	n/a	n/a
16	NFIC	chr4:15480655-15481270	HepG2	liver:	n/a	n/a
17	YY1	chr4:15480549-15481502	SK-N-SH	brain:	n/a	chr4:15481069-15481077
18	TCF12	chr4:15480615-15481449	A549	lung:	n/a	n/a
19	TAF7	chr4:15480650-15481263	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr4:15480579-15481265	Hela-S3	cervix:	n/a	chr4:15480761-15480780
21	CTCF	chr4:15480621-15480917	MCF-7	breast:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
22	RAD21	chr4:15480515-15481533	SK-N-SH_RA	brain:	n/a	chr4:15480761-15480780
23	USF2	chr4:15480671-15481662	Hela-S3	cervix:	n/a	chr4:15481086-15481095 chr4:15481085-15481094 chr4:15481084-15481097 chr4:15481084-15481095
24	CTCF	chr4:15480662-15480896	A549	lung:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
25	RFX5	chr4:15480603-15481932	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr4:15480640-15480790	HRE	kidney:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
27	CTCF	chr4:15480660-15480810	WI-38	lung:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
28	E2F4	chr4:15480663-15480859	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr4:15480647-15481479	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:15480645-15480872	LNCaP	prostate:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
31	ARID3A	chr4:15480650-15481081	HepG2	liver:	n/a	n/a
32	CTCF	chr4:15480620-15480770	GM12875	blood:	n/a	n/a
33	CTCF	chr4:15480640-15480790	HRPEpiC	eye:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
34	YY1	chr4:15480653-15481171	GM12878	blood:	n/a	chr4:15481069-15481077
35	CTCF	chr4:15480646-15480883	HepG2	liver:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
36	CTCF	chr4:15480619-15480914	HepG2	liver:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
37	CTCF	chr4:15480643-15480951	ECC-1	luminal epithelium:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
38	WRNIP1	chr4:15480630-15480916	GM12878	blood:	n/a	n/a
39	CTCF	chr4:15480660-15480810	HBMEC	blood vessel:	n/a	chr4:15480760-15480778 chr4:15480762-15480783
40	MYC	chr4:15480673-15481337	H1-hESC	embryonic stem cell:	n/a	chr4:15481265-15481274 chr4:15481264-15481275 chr4:15481265-15481274 chr4:15481263-15481276 chr4:15481265-15481275 chr4:15481264-15481274 chr4:15481261-15481276 chr4:15481264-15481275 chr4:15481265-15481274
41	CTCF	chr4:15480599-15481111	HCT-116	colon:	n/a	chr4:15480760-15480778 chr4:15481042-15481051 chr4:15480762-15480783
42	MAX	chr4:15480456-15481662	HCT-116	colon:	n/a	chr4:15481265-15481274 chr4:15481264-15481275 chr4:15481265-15481274 chr4:15481263-15481276 chr4:15481265-15481275 chr4:15481264-15481274 chr4:15481261-15481276 chr4:15481264-15481275 chr4:15481265-15481274
43	CTCF	chr4:15480523-15481069	K562	blood:	n/a	chr4:15480760-15480778 chr4:15481042-15481051 chr4:15480762-15480783
44	USF1	chr4:15480605-15481546	HCT-116	colon:	n/a	chr4:15481086-15481095 chr4:15481085-15481094 chr4:15481084-15481095 chr4:15481084-15481097
45	POLR2A	chr4:15480651-15481424	HCT-116	colon:	n/a	n/a
46	RAD21	chr4:15480592-15480979	GM12878	blood:	n/a	chr4:15480761-15480780
47	CTBP2	chr4:15480477-15481425	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr4:15480563-15481531	HepG2	liver:	n/a	chr4:15480761-15480780
49	USF1	chr4:15480635-15481502	A549	lung:	n/a	chr4:15481086-15481095 chr4:15481085-15481094 chr4:15481084-15481095 chr4:15481084-15481097
50	POLR2A	chr4:15480639-15481717	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:15480643-15480693	HL-60	blood:	n/a
2	chr4:15480643-15480693	AoSMC	blood vessel:	n/a
3	chr4:15480643-15480693	HRPEpiC	eye:	n/a
4	chr4:15480643-15480693	A549	lung:	n/a
5	chr4:15480643-15480693	U87	brain:	n/a
6	chr4:15480643-15480693	HUVEC	blood vessel:	n/a
7	chr4:15480643-15480693	MCF10A-Er-Src	breast:	n/a
8	chr4:15480643-15480693	AG09319	gingival:	n/a
9	chr4:15480643-15480693	HCPEpiC	choroid plexus:	n/a
10	chr4:15480643-15480693	LNCaP	prostate:	n/a
11	chr4:15480643-15480693	ECC-1	luminal epithelium:	n/a
12	chr4:15480643-15480693	GM12892	blood:	n/a
13	chr4:15480643-15480693	PANC-1	pancreas:	n/a
14	chr4:15480643-15480693	GM19239	blood:	n/a
15	chr4:15480643-15480693	PrEC	prostate:	n/a
16	chr4:15480643-15480693	AG04449	skin:	fetal
17	chr4:15480643-15480693	CMK	blood:	n/a
18	chr4:15480643-15480693	SK-N-MC	brain:	n/a
19	chr4:15480643-15480693	HNPCEpiC	eye:	n/a
20	chr4:15480643-15480693	HRE	kidney:	n/a
21	chr4:15480643-15480693	AG04450	lung:	fetal
22	chr4:15480643-15480693	SK-N-SH_RA	brain:	n/a
23	chr4:15480643-15480693	K562	blood:	n/a
24	chr4:15480643-15480693	NB4	blood:	n/a
25	chr4:15480643-15480693	MCF-7	breast:	n/a
26	chr4:15480643-15480693	RPTEC	kidney:	n/a
27	chr4:15480643-15480693	ovcar-3	ovarian:	n/a
28	chr4:15480643-15480693	IMR90	lung:	fetal
29	chr4:15480643-15480693	AG10803	skin:	n/a
30	chr4:15480643-15480693	T-47D	breast:	n/a
31	chr4:15480643-15480693	ProgFib	skin:	n/a
32	chr4:15480643-15480693	NHDF-neo	bronchial:	n/a
33	chr4:15480643-15480693	HIPEpiC	eye:	n/a
34	chr4:15480643-15480693	Hela-S3	cervix:	n/a
35	chr4:15480643-15480693	AG09309	skin:	n/a
36	chr4:15480643-15480693	GM12891	blood:	n/a
37	chr4:15480643-15480693	H1-hESC	embryonic stem cell:	embryo
38	chr4:15480643-15480693	GM06990	blood:	n/a
39	chr4:15480643-15480693	BE2_C	brain:	n/a
40	chr4:15480643-15480693	PFSK-1	brain:	n/a
41	chr4:15480643-15480693	HepG2	liver:	n/a
42	chr4:15480643-15480693	HCM	heart:	n/a
43	chr4:15480643-15480693	BJ	skin:	n/a
44	chr4:15480643-15480693	HCF	heart:	n/a
45	chr4:15480643-15480693	SAEC	small airway:	n/a
46	chr4:15480643-15480693	HPAEpiC	pulmonary alveolar:	n/a
47	chr4:15480643-15480693	HEEpiC	esophagus:	n/a
48	chr4:15480643-15480693	HEK293	kidney:	embryo
49	chr4:15480643-15480693	HCT-116	colon:	n/a
50	chr4:15480643-15480693	Hepatocyte	liver:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:15479978..15480805-chr4:16002697..16003703,3	K562	blood:
2	chr4:15479910..15482087-chr4:15683434..15685124,3	MCF-7	breast:
3	chr4:15479740..15482605-chr4:15655501..15658427,3	MCF-7	breast:
4	chr4:15471401..15472981-chr4:15479809..15481384,2	MCF-7	breast:

Variant related genes	Relation type
CC2D2A	TF binding region
CC2D2A	CpG island
ENSG00000237765	Chromatin interaction
ENSG00000118564	Chromatin interaction
ENSG00000048342	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12642505	0.80[ASN][1000 genomes]
rs12649187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12649193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2314589	0.82[ASN][1000 genomes]
rs59402503	0.89[ASN][1000 genomes]
rs961734	0.82[CHB][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15471800-15480800	Weak transcription	Pancreas	Pancrea
2	chr4:15471800-15481000	Weak transcription	Spleen	Spleen
3	chr4:15472200-15480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr4:15472200-15480800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:15472200-15480800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:15472200-15480800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:15472200-15480800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:15472200-15480800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:15472200-15480800	Weak transcription	Lung	lung
10	chr4:15472600-15480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:15472800-15480800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:15472800-15480800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:15472800-15480800	Weak transcription	NHLF	lung
14	chr4:15473000-15480800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:15473000-15480800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:15473000-15480800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:15473000-15480800	Weak transcription	Fetal Kidney	kidney
18	chr4:15473000-15480800	Weak transcription	Psoas Muscle	Psoas
19	chr4:15473200-15480800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:15473200-15480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:15473200-15480800	Weak transcription	Fetal Heart	heart
22	chr4:15473200-15480800	Weak transcription	Fetal Lung	lung
23	chr4:15473200-15480800	Weak transcription	Fetal Stomach	stomach
24	chr4:15473200-15480800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:15474000-15480800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:15475400-15480800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr4:15476000-15480800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:15478200-15480800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:15478200-15480800	Weak transcription	Aorta	Aorta
30	chr4:15478200-15480800	Weak transcription	Ovary	ovary
31	chr4:15478400-15480800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr4:15478400-15480800	Weak transcription	Adipose Nuclei	Adipose
33	chr4:15478400-15480800	Weak transcription	Liver	Liver
34	chr4:15478400-15480800	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:15478400-15480800	Weak transcription	Left Ventricle	heart
36	chr4:15478600-15480800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:15478600-15480800	Weak transcription	Colon Smooth Muscle	Colon
38	chr4:15479200-15480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:15480400-15480800	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:15480400-15480800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:15480600-15480800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr4:15480600-15480800	Enhancers	K562	blood
43	chr4:15480600-15480800	Active TSS	NH-A	brain
44	chr4:15480600-15481000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr4:15480600-15481000	Active TSS	HUVEC	blood vessel
46	chr4:15480600-15481200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:15480600-15481200	Active TSS	Brain Angular Gyrus	brain
48	chr4:15480600-15481400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr4:15480600-15481400	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr4:15480600-15481400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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