Variant report

Variant	rs28558196
Chromosome Location	chr4:7880360-7880361
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:7873958..7875776-chr4:7879371..7881105,2	MCF-7	breast:
2	chr4:7870109..7872064-chr4:7879515..7881205,2	MCF-7	breast:
3	chr4:7880346..7881907-chr4:7891729..7893475,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

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

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

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

Chromatin state (count:82 , 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	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
7	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
9	chr4:7874600-7881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:7875800-7881000	Weak transcription	Stomach Mucosa	stomach
14	chr4:7876000-7880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
16	chr4:7876800-7881800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:7876800-7885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:7877000-7883200	Enhancers	Colon Smooth Muscle	Colon
19	chr4:7877400-7883200	Enhancers	Fetal Heart	heart
20	chr4:7877400-7885000	Enhancers	NH-A	brain
21	chr4:7877800-7881400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:7877800-7883200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr4:7877800-7883200	Enhancers	Fetal Stomach	stomach
24	chr4:7877800-7883200	Enhancers	Ovary	ovary
25	chr4:7877800-7883200	Enhancers	HSMM	muscle
26	chr4:7877800-7883400	Enhancers	Fetal Muscle Leg	muscle
27	chr4:7878000-7881000	Enhancers	Right Atrium	heart
28	chr4:7878000-7881200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:7878000-7882400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:7878000-7883000	Enhancers	HSMMtube	muscle
31	chr4:7878000-7883200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:7878200-7880400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:7878200-7881000	Enhancers	Brain Germinal Matrix	brain
34	chr4:7878200-7882800	Weak transcription	Placenta	Placenta
35	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:7878400-7880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:7878400-7880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:7878400-7881000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:7878400-7881000	Weak transcription	HepG2	liver
40	chr4:7878400-7881400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr4:7878400-7886600	Weak transcription	Small Intestine	intestine
42	chr4:7878600-7881200	Weak transcription	Fetal Lung	lung
43	chr4:7878600-7883200	Enhancers	HUVEC	blood vessel
44	chr4:7878800-7881600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:7879000-7880800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:7879000-7881600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:7879000-7888200	Weak transcription	Fetal Intestine Large	intestine
48	chr4:7879200-7880600	Weak transcription	NHLF	lung
49	chr4:7879200-7882400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:7879400-7880800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links