Variant report

Variant	rs28417050
Chromosome Location	chr4:7883077-7883078
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	chr4:7881697..7884478-chr4:7901263..7903029,2	MCF-7	breast:

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

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
3	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
8	chr4:7876800-7885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr4:7877000-7883200	Enhancers	Colon Smooth Muscle	Colon
10	chr4:7877400-7883200	Enhancers	Fetal Heart	heart
11	chr4:7877400-7885000	Enhancers	NH-A	brain
12	chr4:7877800-7883200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr4:7877800-7883200	Enhancers	Fetal Stomach	stomach
14	chr4:7877800-7883200	Enhancers	Ovary	ovary
15	chr4:7877800-7883200	Enhancers	HSMM	muscle
16	chr4:7877800-7883400	Enhancers	Fetal Muscle Leg	muscle
17	chr4:7878000-7883200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:7878400-7886600	Weak transcription	Small Intestine	intestine
20	chr4:7878600-7883200	Enhancers	HUVEC	blood vessel
21	chr4:7879000-7888200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:7879400-7883200	Enhancers	Rectal Smooth Muscle	rectum
23	chr4:7879400-7883600	Weak transcription	HMEC	breast
24	chr4:7879400-7888000	Weak transcription	Fetal Brain Female	brain
25	chr4:7879400-7891800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:7879800-7883200	Enhancers	Left Ventricle	heart
27	chr4:7879800-7886800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:7880200-7884800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:7880400-7888000	Weak transcription	Brain Anterior Caudate	brain
30	chr4:7880600-7883200	Enhancers	NHLF	lung
31	chr4:7880600-7883600	Enhancers	Fetal Muscle Trunk	muscle
32	chr4:7880800-7883200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:7880800-7883200	Enhancers	Pancreas	Pancrea
34	chr4:7880800-7883400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:7881000-7883200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr4:7881000-7883200	Enhancers	Stomach Smooth Muscle	stomach
37	chr4:7881000-7887200	Weak transcription	Brain Germinal Matrix	brain
38	chr4:7881200-7885800	Enhancers	Osteobl	bone
39	chr4:7881200-7887000	Weak transcription	Aorta	Aorta
40	chr4:7881200-7887200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr4:7881200-7888200	Weak transcription	Psoas Muscle	Psoas
42	chr4:7881200-7888400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:7881400-7884200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:7881400-7886600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:7881400-7887000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:7881600-7883200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr4:7881800-7883200	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr4:7881800-7884000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr4:7881800-7889800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:7881800-7896600	Weak transcription	Lung	lung

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