Variant report

Variant	rs62289340
Chromosome Location	chr4:7879027-7879028
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	chr4:7878920-7879070	GM06990	blood:	n/a	n/a
2	GATA2	chr4:7878875-7879661	HUVEC	blood vessel:	n/a	n/a
3	MAFK	chr4:7878996-7879141	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7877407..7880268-chr4:7886566..7889549,2	MCF-7	breast:

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11732100	0.90[EUR][1000 genomes]
rs11735005	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130704	0.96[AMR][1000 genomes];1.00[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];0.94[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];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28417050	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28437157	0.96[AMR][1000 genomes];0.99[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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28544299	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28558196	0.97[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	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28694545	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28766602	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34033399	0.94[AMR][1000 genomes];0.99[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	0.80[EUR][1000 genomes]
rs55844411	0.86[AMR][1000 genomes];0.96[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];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289322	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289333	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289335	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289336	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289337	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289339	0.97[AMR][1000 genomes];1.00[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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290571	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.89[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	0.80[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815298	0.84[AMR][1000 genomes];0.96[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];0.96[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];0.97[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];0.95[EUR][1000 genomes]
rs73214042	0.89[EUR][1000 genomes]
rs7378072	0.83[EUR][1000 genomes]
rs7663026	0.96[AMR][1000 genomes];0.99[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];0.99[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
rs62289340	AFAP1	cis	Whole Blood	GTEx
rs62289340	AFAP1	cis	Esophagus Mucosa	GTEx
rs62289340	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 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	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:7873400-7880000	Weak transcription	Lung	lung
8	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
9	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:7874400-7880200	Weak transcription	Gastric	stomach
11	chr4:7874400-7880200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
13	chr4:7874600-7879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:7874600-7880000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:7874600-7881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:7875800-7881000	Weak transcription	Stomach Mucosa	stomach
20	chr4:7876000-7879200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:7876000-7880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
23	chr4:7876800-7880200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:7876800-7881800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:7876800-7885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:7877000-7879600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:7877000-7883200	Enhancers	Colon Smooth Muscle	Colon
28	chr4:7877200-7879800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr4:7877400-7883200	Enhancers	Fetal Heart	heart
30	chr4:7877400-7885000	Enhancers	NH-A	brain
31	chr4:7877600-7879400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:7877600-7879800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr4:7877600-7879800	Enhancers	NHDF-Ad	bronchial
34	chr4:7877800-7879200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr4:7877800-7879200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr4:7877800-7879200	Enhancers	NHLF	lung
37	chr4:7877800-7879400	Enhancers	HMEC	breast
38	chr4:7877800-7879600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr4:7877800-7879600	Enhancers	Osteobl	bone
40	chr4:7877800-7881400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr4:7877800-7883200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr4:7877800-7883200	Enhancers	Fetal Stomach	stomach
43	chr4:7877800-7883200	Enhancers	Ovary	ovary
44	chr4:7877800-7883200	Enhancers	HSMM	muscle
45	chr4:7877800-7883400	Enhancers	Fetal Muscle Leg	muscle
46	chr4:7878000-7879200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:7878000-7879400	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr4:7878000-7881000	Enhancers	Right Atrium	heart
49	chr4:7878000-7881200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr4:7878000-7882400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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