Variant report

Variant	rs62289337
Chromosome Location	chr4:7877939-7877940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:114)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:114 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr4:7877850-7878191	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr4:7877831-7878237	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr4:7877851-7878139	MCF-7	breast:	n/a	n/a
4	RAD21	chr4:7877751-7878175	HepG2	liver:	n/a	n/a
5	CTCF	chr4:7877900-7878050	HFF-Myc	foreskin:	n/a	n/a
6	RAD21	chr4:7877756-7878680	IMR90	lung:	n/a	n/a
7	RAD21	chr4:7877760-7878297	MCF-7	breast:	n/a	n/a
8	CTCF	chr4:7877798-7878219	IMR90	lung:	n/a	n/a
9	CTCF	chr4:7877855-7878035	GM12878	blood:	n/a	n/a
10	RAD21	chr4:7877667-7878562	A549	lung:	n/a	n/a
11	CTCF	chr4:7877838-7878144	MCF-7	breast:	n/a	n/a
12	CTCF	chr4:7877920-7878070	HMF	breast:	n/a	n/a
13	SP1	chr4:7877714-7878281	A549	lung:	n/a	n/a
14	CTCF	chr4:7877900-7878050	MCF-7	breast:	n/a	n/a
15	CTCF	chr4:7877900-7878050	GM12867	blood:	n/a	n/a
16	REST	chr4:7877821-7878152	PANC-1	pancreas:	n/a	n/a
17	REST	chr4:7877855-7878114	PFSK-1	brain:	n/a	n/a
18	RAD21	chr4:7877854-7878211	A549	lung:	n/a	n/a
19	CTCF	chr4:7877900-7878050	HMEC	breast:	n/a	n/a
20	CTCF	chr4:7877680-7878309	A549	lung:	n/a	n/a
21	CTCF	chr4:7877920-7878070	GM06990	blood:	n/a	n/a
22	CTCF	chr4:7877861-7878130	MCF-7	breast:	n/a	n/a
23	RAD21	chr4:7877867-7878170	HepG2	liver:	n/a	n/a
24	CTCF	chr4:7877793-7878230	HepG2	liver:	n/a	n/a
25	CTCF	chr4:7877560-7878983	A549	lung:	n/a	n/a
26	CTCF	chr4:7877834-7878287	MCF-7	breast:	n/a	n/a
27	CTCF	chr4:7877880-7878030	MCF-7	breast:	n/a	n/a
28	CTCF	chr4:7877920-7878070	AoAF	blood vessel:	n/a	n/a
29	POLR2A	chr4:7877887-7878432	HUVEC	blood vessel:	n/a	n/a
30	SMC3	chr4:7877581-7878779	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr4:7877880-7878030	HCT-116	colon:	n/a	n/a
32	MYC	chr4:7877679-7878652	A549	lung:	n/a	n/a
33	REST	chr4:7877902-7878124	Hela-S3	cervix:	n/a	n/a
34	YY1	chr4:7877847-7878323	A549	lung:	n/a	n/a
35	MYC	chr4:7877879-7878056	MCF-7	breast:	n/a	n/a
36	CTCF	chr4:7877920-7878070	WI-38	lung:	n/a	n/a
37	RAD21	chr4:7877802-7878231	MCF-7	breast:	n/a	n/a
38	CTCF	chr4:7877886-7878157	HUVEC	blood vessel:	n/a	n/a
39	REST	chr4:7877858-7878129	MCF-7	breast:	n/a	n/a
40	CTCF	chr4:7877836-7878152	A549	lung:	n/a	n/a
41	CTCF	chr4:7877855-7878154	Gliobla	brain:	n/a	n/a
42	CTCF	chr4:7877929-7878077	GM12891	blood:	n/a	n/a
43	CTCF	chr4:7877880-7878030	RPTEC	kidney:	n/a	n/a
44	REST	chr4:7877908-7878039	K562	blood:	n/a	n/a
45	CTCF	chr4:7877876-7878125	HepG2	liver:	n/a	n/a
46	MAX	chr4:7877667-7878286	A549	lung:	n/a	n/a
47	TCF12	chr4:7877670-7878374	A549	lung:	n/a	n/a
48	REST	chr4:7877877-7878017	PANC-1	pancreas:	n/a	n/a
49	CTCF	chr4:7877920-7878070	SK-N-SH_RA	brain:	n/a	n/a
50	CTCF	chr4:7877894-7878132	Fibrobl	skin:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:7877287..7878806-chr4:7930542..7931312,4	MCF-7	breast:
2	chr4:7877407..7880268-chr4:7886566..7889549,2	MCF-7	breast:
3	chr4:7805394..7806236-chr4:7877431..7878287,4	MCF-7	breast:

No data

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	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130704	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770213	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770321	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17832709	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28417050	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28438948	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28494514	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28544299	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568794	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28600706	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28607519	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28622214	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694545	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28766602	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34033399	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34310670	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55767717	0.81[EUR][1000 genomes]
rs55844411	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56220381	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56229515	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56411722	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61742221	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289320	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289322	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289333	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289335	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289336	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289338	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289339	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289340	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289359	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62290561	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290571	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290574	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290579	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6813758	0.81[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815298	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816389	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6829680	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838073	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6850654	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855532	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73210862	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73210866	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73214041	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7378072	0.84[EUR][1000 genomes]
rs7663026	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680747	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687428	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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
rs62289337	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs62289337	AFAP1	cis	Whole Blood	GTEx
rs62289337	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	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
4	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:7869800-7878000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:7870600-7878000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:7870600-7878000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:7873400-7878800	Weak transcription	Fetal Intestine Small	intestine
11	chr4:7873400-7879000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:7873400-7880000	Weak transcription	Lung	lung
13	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
14	chr4:7873600-7878000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:7873600-7878200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:7873800-7878200	Weak transcription	Fetal Intestine Large	intestine
18	chr4:7874400-7878000	Weak transcription	Fetal Kidney	kidney
19	chr4:7874400-7878000	Weak transcription	Left Ventricle	heart
20	chr4:7874400-7878200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:7874400-7878600	Weak transcription	Fetal Brain Female	brain
22	chr4:7874400-7880200	Weak transcription	Gastric	stomach
23	chr4:7874400-7880200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
25	chr4:7874600-7878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:7874600-7878000	Weak transcription	Aorta	Aorta
27	chr4:7874600-7878000	Weak transcription	Psoas Muscle	Psoas
28	chr4:7874600-7878000	Weak transcription	Right Atrium	heart
29	chr4:7874600-7878200	Weak transcription	Brain Germinal Matrix	brain
30	chr4:7874600-7878600	Weak transcription	Fetal Brain Male	brain
31	chr4:7874600-7879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:7874600-7880000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr4:7874600-7881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:7875600-7878000	Weak transcription	HSMMtube	muscle
38	chr4:7875800-7878000	Weak transcription	Adipose Nuclei	Adipose
39	chr4:7875800-7881000	Weak transcription	Stomach Mucosa	stomach
40	chr4:7876000-7878000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr4:7876000-7878000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:7876000-7878200	Weak transcription	Fetal Lung	lung
43	chr4:7876000-7878800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:7876000-7879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:7876000-7880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
47	chr4:7876600-7878000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:7876800-7878000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr4:7876800-7878000	Enhancers	A549	lung
50	chr4:7876800-7878200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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