Variant report

Variant	rs28622214
Chromosome Location	chr4:7879440-7879441
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	chr4:7873958..7875776-chr4:7879371..7881105,2	MCF-7	breast:
2	chr4:7877407..7880268-chr4:7886566..7889549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11732100	0.90[EUR][1000 genomes]
rs11733177	0.86[TSI][hapmap]
rs11733297	0.85[CEU][hapmap]
rs11735005	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11930623	0.89[TSI][hapmap]
rs12509421	0.85[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs13121514	1.00[JPT][hapmap]
rs13130704	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177036	0.85[CEU][hapmap]
rs17770213	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770321	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17832709	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[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];1.00[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];0.97[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];0.98[EUR][1000 genomes]
rs28558196	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568794	0.99[AMR][1000 genomes];0.96[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];0.98[EUR][1000 genomes];0.96[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];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34310670	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55767717	0.80[EUR][1000 genomes]
rs55844411	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56220381	0.87[AMR][1000 genomes];0.96[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];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61742221	0.99[AMR][1000 genomes];0.97[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289340	0.97[AMR][1000 genomes];1.00[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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290571	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290574	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290579	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6813758	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6814219	0.84[EUR][1000 genomes]
rs6814887	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815298	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816389	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6829680	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6838073	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6850654	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6855532	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73210862	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73210866	0.97[AMR][1000 genomes];0.97[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];0.89[EUR][1000 genomes]
rs7378072	0.83[EUR][1000 genomes]
rs7437940	1.00[YRI][hapmap]
rs7437984	1.00[YRI][hapmap]
rs7663026	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680747	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7687428	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs938604	0.88[YRI][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs28622214	AFAP1	cis	Esophagus Mucosa	GTEx
rs28622214	AFAP1	cis	cerebellum	SCAN
rs28622214	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28622214	AFAP1	cis	Whole Blood	GTEx
rs28622214	ABLIM2	cis	cerebellum	SCAN

Chromatin state (count:86 , 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	chr4:7873400-7880000	Weak transcription	Lung	lung
7	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
8	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:7874400-7880200	Weak transcription	Gastric	stomach
10	chr4:7874400-7880200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
12	chr4:7874600-7879800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:7874600-7880000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:7874600-7881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:7874600-7887600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:7874600-7892800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:7874600-7894000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:7875800-7881000	Weak transcription	Stomach Mucosa	stomach
19	chr4:7876000-7880400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:7876000-7891800	Weak transcription	Hela-S3	cervix
21	chr4:7876800-7880200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:7876800-7881800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:7876800-7885400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:7877000-7879600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr4:7877000-7883200	Enhancers	Colon Smooth Muscle	Colon
26	chr4:7877200-7879800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr4:7877400-7883200	Enhancers	Fetal Heart	heart
28	chr4:7877400-7885000	Enhancers	NH-A	brain
29	chr4:7877600-7879800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr4:7877600-7879800	Enhancers	NHDF-Ad	bronchial
31	chr4:7877800-7879600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr4:7877800-7879600	Enhancers	Osteobl	bone
33	chr4:7877800-7881400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr4:7877800-7883200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:7877800-7883200	Enhancers	Fetal Stomach	stomach
36	chr4:7877800-7883200	Enhancers	Ovary	ovary
37	chr4:7877800-7883200	Enhancers	HSMM	muscle
38	chr4:7877800-7883400	Enhancers	Fetal Muscle Leg	muscle
39	chr4:7878000-7881000	Enhancers	Right Atrium	heart
40	chr4:7878000-7881200	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr4:7878000-7882400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr4:7878000-7883000	Enhancers	HSMMtube	muscle
43	chr4:7878000-7883200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:7878200-7879600	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr4:7878200-7880400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:7878200-7881000	Enhancers	Brain Germinal Matrix	brain
47	chr4:7878200-7882800	Weak transcription	Placenta	Placenta
48	chr4:7878200-7898400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:7878400-7879600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:7878400-7879800	Weak transcription	Left Ventricle	heart

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