Variant report

Variant	rs62290571
Chromosome Location	chr4:7914061-7914062
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	chr4:7913036..7915601-chr4:7939958..7942637,2	MCF-7	breast:
2	chr4:7913753..7915419-chr4:7919599..7921984,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196526	Chromatin interaction
ENSG00000228919	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11732100	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11733297	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11735005	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12509421	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13130704	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17177036	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17770213	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17770321	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17832709	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28375300	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28417050	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28437157	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28438948	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28494514	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28544299	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28558196	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28568794	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28600706	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28607519	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28622214	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28694545	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28766602	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34033399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34310670	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55767717	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55844411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56220381	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56229515	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56411722	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61742221	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62289320	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62289322	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62289333	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62289335	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62289336	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289337	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289338	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289339	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289340	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289359	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62290561	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290573	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62290574	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62290579	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6813758	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6814887	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6815298	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816389	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6829680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838073	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6850654	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855532	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73210862	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73210866	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73214041	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73214042	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7663026	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680747	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7687428	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[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
rs62290571	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs62290571	AFAP1	cis	Esophagus Mucosa	GTEx
rs62290571	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
4	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
5	chr4:7906000-7914200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:7906200-7914400	Enhancers	HUVEC	blood vessel
7	chr4:7907800-7914200	Enhancers	Brain Germinal Matrix	brain
8	chr4:7907800-7935800	Weak transcription	Right Ventricle	heart
9	chr4:7909200-7925400	Weak transcription	Hela-S3	cervix
10	chr4:7910800-7914200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:7911000-7914200	Enhancers	HMEC	breast
12	chr4:7911200-7914400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:7911200-7917000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:7911400-7914400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr4:7911400-7917400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:7912000-7918000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:7912000-7931200	Weak transcription	Aorta	Aorta
18	chr4:7912600-7914600	Weak transcription	HepG2	liver
19	chr4:7912600-7917000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr4:7912600-7917200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:7912800-7914200	Enhancers	Fetal Kidney	kidney
22	chr4:7912800-7914200	Enhancers	HSMMtube	muscle
23	chr4:7912800-7931200	Weak transcription	Gastric	stomach
24	chr4:7913000-7914200	Enhancers	NH-A	brain
25	chr4:7913000-7914800	Enhancers	NHLF	lung
26	chr4:7913000-7927600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:7913000-7930600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:7913000-7931000	Weak transcription	Fetal Intestine Large	intestine
29	chr4:7913200-7914400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr4:7913200-7914800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr4:7913200-7917400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:7913200-7918200	Weak transcription	Colonic Mucosa	Colon
33	chr4:7913200-7919400	Weak transcription	Right Atrium	heart
34	chr4:7913200-7919600	Weak transcription	Lung	lung
35	chr4:7913200-7926400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:7913400-7914200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr4:7913400-7914200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:7913400-7914200	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:7913400-7914200	Genic enhancers	HSMM	muscle
40	chr4:7913400-7914200	Flanking Active TSS	NHDF-Ad	bronchial
41	chr4:7913400-7914400	Enhancers	Fetal Heart	heart
42	chr4:7913400-7914600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:7913400-7914600	Weak transcription	Ovary	ovary
44	chr4:7913400-7917800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr4:7913400-7918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:7913400-7918800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr4:7913400-7919800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr4:7913600-7914200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr4:7913600-7915000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:7913600-7915000	Enhancers	Colon Smooth Muscle	Colon

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