Variant report

Variant	rs62290561
Chromosome Location	chr4:7906329-7906330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11732100	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11733297	0.83[EUR][1000 genomes]
rs11735005	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12509421	0.82[EUR][1000 genomes]
rs13130704	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17177036	0.81[EUR][1000 genomes]
rs17770213	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770321	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17832709	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28375300	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28417050	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28437157	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28438948	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28494514	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28544299	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28558196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28568794	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28600706	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28607519	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28622214	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28694545	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28766602	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34033399	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34310670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55767717	0.83[EUR][1000 genomes]
rs55844411	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56220381	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56229515	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56411722	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61742221	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62289320	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62289322	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289333	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289335	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62289336	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289337	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289338	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289339	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289340	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289359	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62290571	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290574	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290579	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6813758	0.83[EUR][1000 genomes]
rs6814219	0.81[EUR][1000 genomes]
rs6814887	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815298	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816389	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6829680	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838073	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6850654	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855532	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73210862	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210866	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73214041	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73214042	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7378072	0.80[EUR][1000 genomes]
rs7663026	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7680747	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7687428	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[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
rs62290561	AFAP1	cis	Whole Blood	GTEx
rs62290561	AFAP1	cis	Esophagus Mucosa	GTEx
rs62290561	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
2	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
3	chr4:7896800-7907600	Weak transcription	Fetal Intestine Small	intestine
4	chr4:7897000-7907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:7899600-7907000	Enhancers	Fetal Brain Male	brain
6	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:7900000-7906400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:7900000-7907400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:7900200-7912400	Weak transcription	NHEK	skin
10	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:7901000-7907400	Enhancers	HSMMtube	muscle
12	chr4:7901000-7909000	Enhancers	Fetal Brain Female	brain
13	chr4:7901400-7909400	Enhancers	Fetal Lung	lung
14	chr4:7901600-7907400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
16	chr4:7902000-7909200	Enhancers	Fetal Heart	heart
17	chr4:7902000-7909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:7902400-7907600	Enhancers	Rectal Smooth Muscle	rectum
19	chr4:7902600-7906400	Genic enhancers	HSMM	muscle
20	chr4:7903000-7906600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:7903200-7906600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:7903200-7907400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:7903400-7911400	Weak transcription	Pancreas	Pancrea
24	chr4:7903400-7911600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
26	chr4:7904000-7906800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:7904200-7909400	Enhancers	Right Atrium	heart
28	chr4:7904400-7907400	Enhancers	Fetal Muscle Trunk	muscle
29	chr4:7904400-7909400	Enhancers	NHLF	lung
30	chr4:7904600-7906400	Weak transcription	Esophagus	oesophagus
31	chr4:7904600-7906600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr4:7904600-7907400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:7904600-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:7904600-7910400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr4:7904600-7910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:7904800-7906400	Weak transcription	Placenta	Placenta
37	chr4:7904800-7906600	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:7904800-7906800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr4:7904800-7907400	Weak transcription	Right Ventricle	heart
40	chr4:7904800-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr4:7904800-7910400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:7904800-7911200	Weak transcription	Gastric	stomach
43	chr4:7904800-7912200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:7905000-7906800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:7905000-7906800	Enhancers	HMEC	breast
46	chr4:7905000-7911200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr4:7905200-7906400	Weak transcription	Left Ventricle	heart
48	chr4:7905200-7907800	Weak transcription	Stomach Mucosa	stomach
49	chr4:7905200-7911200	Weak transcription	Small Intestine	intestine
50	chr4:7905200-7911800	Weak transcription	Aorta	Aorta

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