Variant report

Variant	rs3749543
Chromosome Location	chr4:16227781-16227782
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	chr4:16227517-16229201	MCF-7	breast:	n/a	n/a
2	CTCF	chr4:16227720-16227870	GM12874	blood:	n/a	n/a
3	POLR2A	chr4:16227518-16229442	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:16227404-16229475	GM18526	blood:	n/a	n/a
5	POLR2A	chr4:16227539-16228863	HEK293	kidney:	n/a	n/a
6	UBTF	chr4:16227470-16229465	K562	blood:	n/a	n/a
7	SIN3AK20	chr4:16227456-16228400	K562	blood:	n/a	n/a
8	HEY1	chr4:16227474-16228546	HepG2	liver:	n/a	n/a
9	HA-E2F1	chr4:16227309-16227939	MCF-7	breast:	n/a	chr4:16227816-16227825
10	TCF3	chr4:16227454-16228091	GM12878	blood:	n/a	n/a
11	YY1	chr4:16227737-16228600	H1-hESC	embryonic stem cell:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
12	TCF7L2	chr4:16227633-16228990	HCT-116	colon:	n/a	n/a
13	POLR2A	chr4:16227556-16229064	GM10847	blood:	n/a	n/a
14	MAZ	chr4:16227273-16229432	K562	blood:	n/a	chr4:16228103-16228113
15	POLR2A	chr4:16227561-16228748	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr4:16227474-16229038	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr4:16227472-16228475	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr4:16227473-16229161	NB4	blood:	n/a	n/a
19	POLR2A	chr4:16227467-16228542	H1-neurons	neurons:	n/a	n/a
20	MAZ	chr4:16227203-16229671	IMR90	lung:	n/a	chr4:16228103-16228113
21	MXI1	chr4:16227193-16229611	IMR90	lung:	n/a	n/a
22	MAX	chr4:16227353-16228572	ECC-1	luminal epithelium:	n/a	chr4:16228103-16228113
23	POLR2A	chr4:16226799-16229901	GM12891	blood:	n/a	n/a
24	TAF1	chr4:16227527-16228560	K562	blood:	n/a	n/a
25	MAX	chr4:16227571-16229498	K562	blood:	n/a	chr4:16228103-16228113
26	POLR2A	chr4:16227458-16229614	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr4:16227469-16228056	Hela-S3	cervix:	n/a	n/a
28	PAX5	chr4:16227507-16228492	GM12892	blood:	n/a	chr4:16227812-16227821
29	TBP	chr4:16227326-16229601	K562	blood:	n/a	n/a
30	MAX	chr4:16227397-16229058	HepG2	liver:	n/a	chr4:16228103-16228113
31	POLR2A	chr4:16227284-16229859	MCF10A-Er-Src	breast:	n/a	n/a
32	MAX	chr4:16227318-16228854	NB4	blood:	n/a	chr4:16228103-16228113
33	MAX	chr4:16227465-16229097	K562	blood:	n/a	chr4:16228103-16228113
34	MXI1	chr4:16227474-16229045	HepG2	liver:	n/a	n/a
35	TBP	chr4:16227543-16229131	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZBTB7A	chr4:16227445-16227902	ECC-1	luminal epithelium:	n/a	n/a
37	YY1	chr4:16227485-16229140	HepG2	liver:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
38	YY1	chr4:16227524-16228697	SK-N-SH_RA	brain:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
39	YY1	chr4:16227604-16228758	SK-N-SH	brain:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
40	POLR2A	chr4:16226421-16229959	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr4:16227346-16229569	Hela-S3	cervix:	n/a	n/a
42	YY1	chr4:16227607-16228849	GM12878	blood:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
43	POLR2A	chr4:16227550-16229081	ECC-1	luminal epithelium:	n/a	n/a
44	YY1	chr4:16227536-16228989	GM12878	blood:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
45	HCFC1	chr4:16226663-16228826	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr4:16227368-16229531	GM12892	blood:	n/a	n/a
47	YY1	chr4:16227733-16228907	SK-N-SH_RA	brain:	n/a	chr4:16228102-16228111 chr4:16227813-16227824 chr4:16228816-16228830 chr4:16228071-16228088 chr4:16227813-16227822 chr4:16228133-16228147 chr4:16227816-16227825
48	POLR2A	chr4:16227393-16229566	GM18951	blood:	n/a	n/a
49	CHD2	chr4:16227751-16227906	GM12878	blood:	n/a	n/a
50	MYC	chr4:16227418-16229000	K562	blood:	n/a	chr4:16228103-16228113

No.	Distal block	Cell Line	Cell type
1	chr4:16212529..16219737-chr4:16225844..16229602,8	MCF-7	breast:
2	chr4:16216932..16218804-chr4:16227245..16229857,2	MCF-7	breast:
3	chr4:15002785..15006911-chr4:16226901..16230678,5	K562	blood:
4	chr21:33104183..33104701-chr4:16227636..16228281,2	Hela-S3	cervix:
5	chr4:15681714..15684664-chr4:16226494..16229781,3	K562	blood:
6	chr17:59476916..59479068-chr4:16227271..16228837,2	MCF-7	breast:

Variant related genes	Relation type
TAPT1-AS1	TF binding region
TAPT1	TF binding region
ENSG00000118564	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000137449	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000247624	Chromatin interaction
ENSG00000156304	Chromatin interaction
ENSG00000169762	Chromatin interaction
ENSG00000237765	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1025897	0.82[ASN][1000 genomes]
rs10939657	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13133263	0.81[ASN][1000 genomes]
rs4317201	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6812660	0.83[ASN][1000 genomes]
rs961449	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004821	chr4:16055996-16830629	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537046	chr4:16055996-16830629	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv537047	chr4:16182060-16375787	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv878720	chr4:16222046-16242215	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv537048	chr4:16226406-16375787	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3405372	chr4:16226679-16229727	Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv3489117	chr4:16226904-16229802	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3489118	chr4:16226904-16229802	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv20417	chr4:16227560-16228537	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv593771	chr4:16227587-16228240	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv593772	chr4:16227594-16228240	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
12	nsv593773	chr4:16227594-16228293	Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv593774	chr4:16227594-16228345	Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv593775	chr4:16227594-16228416	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv593776	chr4:16227709-16228416	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv593777	chr4:16227777-16228416	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:16225600-16230800	Active TSS	A549	lung
2	chr4:16225800-16230000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:16226200-16229600	Active TSS	Right Atrium	heart
4	chr4:16226400-16228400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:16226400-16228800	Active TSS	Primary T cells fromperipheralblood	blood
6	chr4:16226400-16228800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:16226400-16228800	Active TSS	Fetal Thymus	thymus
8	chr4:16226400-16228800	Active TSS	Thymus	Thymus
9	chr4:16226400-16229000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr4:16226400-16229200	Active TSS	Fetal Stomach	stomach
11	chr4:16226400-16229400	Active TSS	Aorta	Aorta
12	chr4:16226400-16229400	Active TSS	HepG2	liver
13	chr4:16226400-16229600	Active TSS	Left Ventricle	heart
14	chr4:16226400-16229600	Active TSS	Psoas Muscle	Psoas
15	chr4:16226400-16229800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:16226400-16229800	Active TSS	Right Ventricle	heart
17	chr4:16226400-16229800	Active TSS	Stomach Smooth Muscle	stomach
18	chr4:16226400-16230600	Active TSS	GM12878-XiMat	blood
19	chr4:16226600-16228600	Active TSS	Fetal Muscle Leg	muscle
20	chr4:16226600-16228800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr4:16226600-16228800	Active TSS	NH-A	brain
22	chr4:16226600-16229000	Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr4:16226600-16229200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:16226600-16229200	Active TSS	Fetal Intestine Small	intestine
25	chr4:16226600-16229400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:16226600-16229400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr4:16226600-16229400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:16226600-16229400	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr4:16226600-16229600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:16226600-16229600	Active TSS	HMEC	breast
31	chr4:16226600-16229800	Active TSS	H1 Cell Line	embryonic stem cell
32	chr4:16226600-16229800	Active TSS	NHDF-Ad	bronchial
33	chr4:16226600-16230000	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr4:16226600-16230800	Active TSS	K562	blood
35	chr4:16226800-16227800	Active TSS	Fetal Lung	lung
36	chr4:16226800-16228600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:16226800-16228800	Active TSS	Fetal Muscle Trunk	muscle
38	chr4:16226800-16229000	Active TSS	HSMM	muscle
39	chr4:16226800-16229200	Active TSS	NHLF	lung
40	chr4:16226800-16229400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:16226800-16229400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:16226800-16229600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr4:16226800-16229600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:16226800-16229600	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr4:16226800-16229600	Active TSS	Ovary	ovary
46	chr4:16226800-16229800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr4:16226800-16230000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:16226800-16230600	Active TSS	Brain Anterior Caudate	brain
49	chr4:16227000-16227800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:16227000-16227800	Active TSS	Fetal Kidney	kidney

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