Variant report

Variant	rs28437157
Chromosome Location	chr4:7874435-7874436
allele	A/C
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	TEAD4	chr4:7873754-7874644	SK-N-SH	brain:	n/a	n/a
2	MAX	chr4:7873497-7874635	A549	lung:	n/a	n/a
3	TCF12	chr4:7873602-7874784	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr4:7873887-7874602	Hela-S3	cervix:	n/a	n/a
5	PBX3	chr4:7873819-7874610	SK-N-SH	brain:	n/a	n/a
6	MAX	chr4:7873849-7874592	ECC-1	luminal epithelium:	n/a	n/a
7	STAT3	chr4:7873665-7874580	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr4:7873909-7874549	Hela-S3	cervix:	n/a	n/a
9	BRCA1	chr4:7873626-7874622	Hela-S3	cervix:	n/a	n/a
10	FOXA2	chr4:7873979-7874509	A549	lung:	n/a	n/a
11	GATA3	chr4:7873669-7874673	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr4:7873858-7874577	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr4:7873760-7874521	A549	lung:	n/a	n/a
14	TCF12	chr4:7873850-7874609	ECC-1	luminal epithelium:	n/a	n/a
15	MAFK	chr4:7873837-7874585	IMR90	lung:	n/a	chr4:7874407-7874422 chr4:7874014-7874030
16	NFIC	chr4:7873749-7874628	ECC-1	luminal epithelium:	n/a	n/a
17	MAFK	chr4:7874430-7874462	HepG2	liver:	n/a	n/a
18	NFIC	chr4:7873710-7874717	SK-N-SH	brain:	n/a	n/a
19	FOSL2	chr4:7873846-7874502	A549	lung:	n/a	chr4:7874088-7874097
20	MAX	chr4:7873823-7874643	SK-N-SH	brain:	n/a	n/a
21	RFX5	chr4:7873745-7874631	Hela-S3	cervix:	n/a	n/a
22	TCF7L2	chr4:7874009-7874513	Hela-S3	cervix:	n/a	n/a
23	MAFK	chr4:7873687-7874666	Hela-S3	cervix:	n/a	chr4:7874407-7874422 chr4:7874014-7874030
24	MAFK	chr4:7874364-7874444	HepG2	liver:	n/a	chr4:7874407-7874422
25	TEAD4	chr4:7873852-7874571	ECC-1	luminal epithelium:	n/a	n/a
26	JUND	chr4:7873788-7874640	Hela-S3	cervix:	n/a	chr4:7874088-7874097
27	GATA3	chr4:7873764-7874696	SK-N-SH	brain:	n/a	n/a
28	SP1	chr4:7873469-7874679	A549	lung:	n/a	n/a
29	MAX	chr4:7873956-7874538	ECC-1	luminal epithelium:	n/a	n/a
30	MXI1	chr4:7873924-7874595	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr4:7874360-7874510	HPF	lung:	n/a	n/a
32	EP300	chr4:7873692-7874646	A549	lung:	n/a	chr4:7873817-7873831
33	TCF12	chr4:7873788-7874627	ECC-1	luminal epithelium:	n/a	n/a
34	TEAD4	chr4:7874044-7874553	A549	lung:	n/a	n/a
35	TEAD4	chr4:7873903-7874483	A549	lung:	n/a	n/a
36	GTF2F1	chr4:7873959-7874504	Hela-S3	cervix:	n/a	n/a
37	SMC3	chr4:7873645-7874614	Hela-S3	cervix:	n/a	n/a
38	FOSL2	chr4:7873811-7874589	SK-N-SH	brain:	n/a	chr4:7874088-7874097
39	FOS	chr4:7873992-7874528	MCF10A-Er-Src	breast:	n/a	chr4:7874088-7874097
40	FOXA2	chr4:7873927-7874587	A549	lung:	n/a	n/a
41	GTF3C2	chr4:7873909-7874975	Hela-S3	cervix:	n/a	n/a
42	EP300	chr4:7873802-7874588	ECC-1	luminal epithelium:	n/a	chr4:7873817-7873831
43	JUND	chr4:7873165-7874603	SK-N-SH	brain:	n/a	chr4:7874088-7874097
44	MAX	chr4:7873841-7874560	Hela-S3	cervix:	n/a	n/a
45	MAX	chr4:7873819-7874626	SK-N-SH	brain:	n/a	n/a
46	ZKSCAN1	chr4:7873907-7874575	Hela-S3	cervix:	n/a	n/a
47	EP300	chr4:7873688-7874628	Hela-S3	cervix:	n/a	chr4:7873817-7873831
48	ZNF143	chr4:7874158-7874447	Hela-S3	cervix:	n/a	chr4:7874330-7874345
49	JUN	chr4:7873650-7874569	Hela-S3	cervix:	n/a	chr4:7874088-7874097
50	TCF12	chr4:7873212-7874655	A549	lung:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11732100	0.90[EUR][1000 genomes]
rs11733297	0.80[EUR][1000 genomes]
rs11735005	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130704	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770213	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28438948	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544299	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607519	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55767717	0.81[EUR][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56229515	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56411722	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61742221	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289320	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289322	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289333	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62290573	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290574	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6813758	0.81[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816389	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838073	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210862	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73210866	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214041	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7378072	0.84[EUR][1000 genomes]
rs7663026	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680747	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687428	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28437157	AFAP1	cis	Whole Blood	GTEx
rs28437157	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28437157	AFAP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7865400-7875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:7866000-7875200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:7866000-7875400	Weak transcription	Stomach Mucosa	stomach
5	chr4:7866000-7877600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:7866000-7877800	Weak transcription	HepG2	liver
7	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
9	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:7869600-7877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:7869800-7878000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:7870400-7876800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:7870600-7877200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:7870600-7877200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:7870600-7877600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:7870600-7878000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:7870600-7878000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:7872600-7874600	Enhancers	Fetal Heart	heart
21	chr4:7873000-7875800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr4:7873200-7874600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:7873200-7874600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:7873200-7874600	Enhancers	Placenta	Placenta
25	chr4:7873200-7874600	Flanking Active TSS	Hela-S3	cervix
26	chr4:7873200-7875200	Weak transcription	Colonic Mucosa	Colon
27	chr4:7873400-7874600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:7873400-7874600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:7873400-7874600	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:7873400-7874600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr4:7873400-7874600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr4:7873400-7874600	Enhancers	Brain Germinal Matrix	brain
33	chr4:7873400-7874600	Enhancers	Brain Hippocampus Middle	brain
34	chr4:7873400-7874600	Enhancers	Rectal Smooth Muscle	rectum
35	chr4:7873400-7874600	Flanking Active TSS	A549	lung
36	chr4:7873400-7874600	Flanking Active TSS	HSMM	muscle
37	chr4:7873400-7874800	Enhancers	Adipose Nuclei	Adipose
38	chr4:7873400-7875400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:7873400-7875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:7873400-7875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:7873400-7875800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:7873400-7876000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:7873400-7877200	Weak transcription	Primary T cells from cord blood	blood
44	chr4:7873400-7878800	Weak transcription	Fetal Intestine Small	intestine
45	chr4:7873400-7879000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:7873400-7880000	Weak transcription	Lung	lung
47	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
48	chr4:7873600-7874600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:7873600-7874600	Enhancers	Fetal Stomach	stomach
50	chr4:7873600-7878000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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