Variant report

Variant	rs56411722
Chromosome Location	chr4:7892425-7892426
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	chr4:7880346..7881907-chr4:7891729..7893475,2	MCF-7	breast:
2	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11732100	0.89[EUR][1000 genomes]
rs11735005	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130704	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[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	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438948	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544299	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28607519	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.94[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];0.89[EUR][1000 genomes]
rs61742221	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62289320	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289322	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289333	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.96[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];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.94[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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816389	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838073	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210862	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73210866	0.99[AMR][1000 genomes];0.94[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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680747	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687428	0.97[AMR][1000 genomes];0.97[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
rs56411722	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs56411722	AFAP1	cis	Esophagus Mucosa	GTEx
rs56411722	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr4:7881800-7896600	Weak transcription	Lung	lung
7	chr4:7883200-7893000	Weak transcription	Left Ventricle	heart
8	chr4:7883200-7904400	Weak transcription	Gastric	stomach
9	chr4:7884800-7892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:7886000-7895800	Weak transcription	Esophagus	oesophagus
11	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
12	chr4:7888200-7893000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:7889000-7892600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:7889000-7892600	Weak transcription	Aorta	Aorta
15	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:7889600-7892600	Weak transcription	Fetal Kidney	kidney
17	chr4:7890800-7893000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:7890800-7893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:7891200-7893000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:7891400-7894000	Weak transcription	Fetal Intestine Small	intestine
21	chr4:7891600-7892800	Enhancers	Osteobl	bone
22	chr4:7891600-7894800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:7891600-7894800	Enhancers	Colon Smooth Muscle	Colon
24	chr4:7891600-7895000	Enhancers	NHDF-Ad	bronchial
25	chr4:7891800-7892600	Enhancers	Stomach Mucosa	stomach
26	chr4:7891800-7892600	Enhancers	HUVEC	blood vessel
27	chr4:7891800-7892800	Enhancers	NHLF	lung
28	chr4:7891800-7893000	Enhancers	Brain Anterior Caudate	brain
29	chr4:7891800-7893000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr4:7891800-7893200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:7891800-7893200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr4:7891800-7893400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:7891800-7893400	Enhancers	Ovary	ovary
34	chr4:7891800-7893600	Enhancers	HSMMtube	muscle
35	chr4:7891800-7893800	Enhancers	Stomach Smooth Muscle	stomach
36	chr4:7891800-7894000	Enhancers	Hela-S3	cervix
37	chr4:7891800-7894400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:7891800-7894400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr4:7891800-7894400	Enhancers	Rectal Smooth Muscle	rectum
40	chr4:7891800-7894400	Enhancers	HepG2	liver
41	chr4:7891800-7894400	Enhancers	NHEK	skin
42	chr4:7891800-7894800	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr4:7891800-7894800	Enhancers	Fetal Heart	heart
44	chr4:7891800-7894800	Enhancers	HMEC	breast
45	chr4:7891800-7895000	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:7891800-7895400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr4:7891800-7895800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr4:7892000-7892600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr4:7892000-7892600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:7892000-7893200	Enhancers	Brain Angular Gyrus	brain

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