Variant report

Variant	rs28489592
Chromosome Location	chr4:7897808-7897809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7896306..7899121-chr4:7899762..7902473,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12641498	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139805	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13140108	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13151529	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1317111	0.87[ASN][1000 genomes]
rs1320070	0.85[ASN][1000 genomes]
rs1320071	0.85[ASN][1000 genomes]
rs1320074	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1320075	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13435730	0.87[ASN][1000 genomes]
rs17770447	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17833038	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1878325	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2385898	0.88[ASN][1000 genomes]
rs2385900	0.86[ASN][1000 genomes]
rs2385901	0.88[ASN][1000 genomes]
rs2385902	0.88[ASN][1000 genomes]
rs2385908	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385909	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385910	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28370977	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28464089	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28631205	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28715921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28726254	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28734123	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28752120	0.83[AMR][1000 genomes]
rs28795989	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2891928	0.90[ASN][1000 genomes]
rs34179701	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34317049	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34505548	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34685551	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34701321	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34984446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35661042	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4627847	0.87[ASN][1000 genomes]
rs4696746	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4696778	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696779	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55937650	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57831033	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6811851	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6846317	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6848540	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6857814	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7437940	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7437984	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7441569	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7655918	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7663205	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7686202	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7687431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7694650	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330348	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs938604	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28489592	AFAP1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:7883200-7904400	Weak transcription	Gastric	stomach
3	chr4:7886800-7904400	Weak transcription	Small Intestine	intestine
4	chr4:7889200-7901200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:7892600-7903800	Weak transcription	Stomach Mucosa	stomach
6	chr4:7893000-7902200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:7893200-7903400	Weak transcription	Fetal Kidney	kidney
8	chr4:7893200-7905600	Weak transcription	Brain Angular Gyrus	brain
9	chr4:7893600-7900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:7893800-7902600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:7894200-7901000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:7894200-7902000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
14	chr4:7894400-7898200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:7894400-7900400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:7894400-7901000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:7894400-7901000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:7894400-7901400	Weak transcription	Fetal Lung	lung
19	chr4:7894400-7904400	Weak transcription	Left Ventricle	heart
20	chr4:7894400-7906200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:7894600-7898000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:7894600-7898800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:7894600-7898800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:7894600-7899600	Weak transcription	Ovary	ovary
25	chr4:7894600-7900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:7894600-7901000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:7894600-7902800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:7894800-7899600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:7894800-7900200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:7895000-7898800	Weak transcription	NHDF-Ad	bronchial
31	chr4:7895000-7899000	Weak transcription	NHLF	lung
32	chr4:7895000-7900200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr4:7895000-7901000	Weak transcription	HSMMtube	muscle
34	chr4:7895000-7901200	Weak transcription	HUVEC	blood vessel
35	chr4:7895200-7899400	Enhancers	Fetal Heart	heart
36	chr4:7895600-7898200	Enhancers	Fetal Brain Female	brain
37	chr4:7895600-7907600	Weak transcription	Colonic Mucosa	Colon
38	chr4:7896000-7902600	Weak transcription	Aorta	Aorta
39	chr4:7896200-7898600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:7896400-7899000	Strong transcription	Osteobl	bone
41	chr4:7896400-7899200	Weak transcription	NH-A	brain
42	chr4:7896800-7898000	Enhancers	A549	lung
43	chr4:7896800-7898200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr4:7896800-7898600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:7896800-7899000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:7896800-7899000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:7896800-7899000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:7896800-7899400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:7896800-7901000	Weak transcription	HSMM	muscle
50	chr4:7896800-7901200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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