Variant report

Variant	rs6447872
Chromosome Location	chr4:7943106-7943107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:58)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:58 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr4:7942782-7943189	ECC-1	luminal epithelium:	n/a	n/a
2	PBX3	chr4:7942750-7943434	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr4:7942645-7943600	ECC-1	luminal epithelium:	n/a	n/a
4	STAT3	chr4:7943066-7943263	MCF10A-Er-Src	breast:	n/a	n/a
5	TEAD4	chr4:7942709-7943468	ECC-1	luminal epithelium:	n/a	n/a
6	GATA3	chr4:7942896-7943139	T-47D	breast:	n/a	n/a
7	SP1	chr4:7942665-7943535	HCT-116	colon:	n/a	n/a
8	YY1	chr4:7942810-7943261	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr4:7942823-7943336	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOXA1	chr4:7942962-7943196	T-47D	breast:	n/a	n/a
11	POLR2A	chr4:7942959-7943222	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr4:7943103-7943292	H1-hESC	embryonic stem cell:	n/a	n/a
13	EP300	chr4:7942811-7943152	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr4:7942895-7943214	MCF-7	breast:	n/a	n/a
15	TEAD4	chr4:7942831-7943288	MCF-7	breast:	n/a	n/a
16	MAX	chr4:7942701-7943338	MCF-7	breast:	n/a	n/a
17	NR2F2	chr4:7942670-7943387	MCF-7	breast:	n/a	n/a
18	YY1	chr4:7942956-7943189	H1-hESC	embryonic stem cell:	n/a	n/a
19	FOXA1	chr4:7942878-7943261	ECC-1	luminal epithelium:	n/a	n/a
20	CHD2	chr4:7942874-7943195	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr4:7942822-7943333	MCF-7	breast:	n/a	n/a
22	POLR2A	chr4:7942858-7943248	H1-hESC	embryonic stem cell:	n/a	n/a
23	GATA3	chr4:7942688-7943385	MCF-7	breast:	n/a	n/a
24	MAX	chr4:7942656-7943891	A549	lung:	n/a	n/a
25	RXRA	chr4:7942772-7943441	SK-N-SH	brain:	n/a	n/a
26	MAX	chr4:7942623-7943342	ECC-1	luminal epithelium:	n/a	n/a
27	FOSL2	chr4:7942869-7943527	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr4:7942546-7943394	ECC-1	luminal epithelium:	n/a	chr4:7943201-7943208
29	GATA3	chr4:7942871-7943143	T-47D	breast:	n/a	n/a
30	NFIC	chr4:7942547-7943542	ECC-1	luminal epithelium:	n/a	n/a
31	FOSL2	chr4:7943021-7943498	A549	lung:	n/a	n/a
32	TEAD4	chr4:7942735-7943535	ECC-1	luminal epithelium:	n/a	n/a
33	SP1	chr4:7942813-7943342	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr4:7942914-7943177	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr4:7943030-7943343	Hela-S3	cervix:	n/a	n/a
36	EP300	chr4:7942782-7943218	MCF-7	breast:	n/a	n/a
37	FOXA1	chr4:7942919-7943209	ECC-1	luminal epithelium:	n/a	n/a
38	ZNF263	chr4:7942918-7943352	HEK293-T-REx	kidney:	n/a	chr4:7943052-7943073 chr4:7943120-7943141
39	YY1	chr4:7942912-7943144	HCT-116	colon:	n/a	n/a
40	MAX	chr4:7942779-7943606	ECC-1	luminal epithelium:	n/a	n/a
41	FOXA1	chr4:7942963-7943179	T-47D	breast:	n/a	n/a
42	RAD21	chr4:7942831-7943261	H1-hESC	embryonic stem cell:	n/a	n/a
43	TEAD4	chr4:7942843-7943227	H1-hESC	embryonic stem cell:	n/a	n/a
44	TEAD4	chr4:7942836-7943239	MCF-7	breast:	n/a	n/a
45	ZNF217	chr4:7942830-7943259	MCF-7	breast:	n/a	n/a
46	SP1	chr4:7942807-7943266	H1-hESC	embryonic stem cell:	n/a	n/a
47	TCF12	chr4:7942938-7943169	H1-hESC	embryonic stem cell:	n/a	n/a
48	NFIC	chr4:7942969-7943453	SK-N-SH	brain:	n/a	n/a
49	GATA3	chr4:7942635-7943394	MCF-7	breast:	n/a	n/a
50	HDAC2	chr4:7942798-7943294	MCF-7	breast:	n/a	n/a

No data

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12642714	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1344223	1.00[JPT][hapmap]
rs2385914	1.00[JPT][hapmap]
rs6840305	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6846757	1.00[JPT][hapmap]
rs7695170	1.00[JPT][hapmap]
rs7698368	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6447872	AFAP1	cis	Whole Blood	GTEx
rs6447872	AFAP	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7941600-7943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:7941600-7944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:7941600-7944400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
5	chr4:7941800-7943600	Enhancers	Fetal Heart	heart
6	chr4:7942000-7943200	Enhancers	Esophagus	oesophagus
7	chr4:7942000-7943200	Enhancers	Fetal Muscle Trunk	muscle
8	chr4:7942000-7943200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr4:7942000-7943200	Enhancers	HSMMtube	muscle
10	chr4:7942000-7943400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:7942000-7943400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:7942000-7943400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:7942000-7943400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:7942000-7943400	Enhancers	HMEC	breast
15	chr4:7942000-7943600	Enhancers	Osteobl	bone
16	chr4:7942000-7943800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr4:7942000-7943800	Enhancers	Adipose Nuclei	Adipose
18	chr4:7942000-7943800	Enhancers	Pancreas	Pancrea
19	chr4:7942000-7943800	Enhancers	Stomach Mucosa	stomach
20	chr4:7942000-7943800	Enhancers	HepG2	liver
21	chr4:7942000-7943800	Enhancers	HSMM	muscle
22	chr4:7942000-7944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:7942000-7944000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:7942000-7944200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:7942000-7944200	Enhancers	Fetal Intestine Large	intestine
26	chr4:7942000-7944200	Enhancers	NHDF-Ad	bronchial
27	chr4:7942000-7944400	Enhancers	Fetal Intestine Small	intestine
28	chr4:7942000-7944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:7942000-7945200	Enhancers	A549	lung
30	chr4:7942000-7945400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:7942000-7945400	Enhancers	Placenta	Placenta
32	chr4:7942000-7945400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr4:7942000-7946200	Weak transcription	Liver	Liver
34	chr4:7942000-7946400	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:7942000-7946400	Weak transcription	Fetal Stomach	stomach
36	chr4:7942000-7950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr4:7942200-7943200	Enhancers	HUVEC	blood vessel
40	chr4:7942200-7943400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr4:7942200-7943400	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr4:7942200-7943600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:7942200-7943800	Enhancers	H9 Cell Line	embryonic stem cell
44	chr4:7942200-7944000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:7942200-7944000	Enhancers	NHEK	skin
46	chr4:7942200-7944800	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:7942200-7947400	Weak transcription	Fetal Brain Male	brain
48	chr4:7942200-7950600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr4:7942600-7943400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:7942600-7943400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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