Variant report

Variant	rs62289336
Chromosome Location	chr4:7877661-7877662
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	CTCF	chr4:7877560-7878983	A549	lung:	n/a	n/a
2	SMC3	chr4:7877581-7878779	SK-N-SH	brain:	n/a	n/a
3	STAT3	chr4:7877474-7877674	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr4:7877617-7878631	A549	lung:	n/a	n/a

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:

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	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130704	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770213	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770321	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17832709	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375300	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28417050	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437157	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28438948	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28494514	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28544299	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568794	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28600706	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28607519	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28622214	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694545	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28766602	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34033399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34310670	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55767717	0.81[EUR][1000 genomes]
rs55844411	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56220381	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56229515	0.90[EUR][1000 genomes]
rs56411722	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61742221	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62289320	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289322	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289333	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289337	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289338	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289339	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289340	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289359	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62290561	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290571	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290574	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290579	0.90[EUR][1000 genomes]
rs6813758	0.81[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815298	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816389	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6829680	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838073	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6850654	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855532	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73210862	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73210866	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73214041	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73214042	0.88[EUR][1000 genomes]
rs7378072	0.84[EUR][1000 genomes]
rs7663026	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687428	0.99[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
rs62289336	AFAP1	cis	Esophagus Mucosa	GTEx
rs62289336	AFAP1	cis	Whole Blood	GTEx
rs62289336	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7866000-7877800	Weak transcription	HepG2	liver
3	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
5	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:7869800-7878000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr4:7870600-7878000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:7870600-7878000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:7873400-7878800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:7873400-7879000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr4:7873400-7880000	Weak transcription	Lung	lung
14	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
15	chr4:7873600-7878000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:7873600-7878200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:7873800-7878200	Weak transcription	Fetal Intestine Large	intestine
19	chr4:7874200-7877800	Weak transcription	Ovary	ovary
20	chr4:7874400-7877800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:7874400-7878000	Weak transcription	Fetal Kidney	kidney
22	chr4:7874400-7878000	Weak transcription	Left Ventricle	heart
23	chr4:7874400-7878200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:7874400-7878600	Weak transcription	Fetal Brain Female	brain
25	chr4:7874400-7880200	Weak transcription	Gastric	stomach
26	chr4:7874400-7880200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
28	chr4:7874600-7877800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:7874600-7877800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:7874600-7877800	Weak transcription	Placenta	Placenta
31	chr4:7874600-7877800	Weak transcription	Fetal Stomach	stomach
32	chr4:7874600-7877800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:7874600-7877800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr4:7874600-7877800	Weak transcription	NHLF	lung
35	chr4:7874600-7878000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:7874600-7878000	Weak transcription	Aorta	Aorta
37	chr4:7874600-7878000	Weak transcription	Psoas Muscle	Psoas
38	chr4:7874600-7878000	Weak transcription	Right Atrium	heart
39	chr4:7874600-7878200	Weak transcription	Brain Germinal Matrix	brain
40	chr4:7874600-7878600	Weak transcription	Fetal Brain Male	brain
41	chr4:7874600-7879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:7874600-7880000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr4:7874600-7881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:7874800-7877800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:7874800-7877800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:7875600-7878000	Weak transcription	HSMMtube	muscle
50	chr4:7875800-7877800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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