Variant report

Variant	rs56220381
Chromosome Location	chr4:7907636-7907637
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	chr4:7891241..7895444-chr4:7905345..7908483,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11732100	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11733297	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11735005	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12509421	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130704	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17177036	0.80[EUR][1000 genomes]
rs17770213	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770321	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28375300	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28417050	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28438948	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28494514	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28544299	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28558196	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28600706	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28607519	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28622214	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28766602	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34033399	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55767717	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55844411	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56229515	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56411722	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61742221	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62289320	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289322	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289333	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62289335	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62290561	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62290571	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62290573	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290574	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62290579	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6813758	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6814219	0.80[EUR][1000 genomes]
rs6814887	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815298	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6816389	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6829680	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6838073	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6850654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6855532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73210862	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73210866	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73214041	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73214042	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7663026	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7680747	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7687428	0.86[AMR][1000 genomes];0.96[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
rs56220381	AFAP1	cis	Esophagus Mucosa	GTEx
rs56220381	AFAP1	cis	Whole Blood	GTEx
rs56220381	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7894200-7912400	Weak transcription	Fetal Intestine Large	intestine
2	chr4:7899800-7930600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:7900200-7912400	Weak transcription	NHEK	skin
4	chr4:7900800-7914400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr4:7901000-7909000	Enhancers	Fetal Brain Female	brain
6	chr4:7901400-7909400	Enhancers	Fetal Lung	lung
7	chr4:7901600-7914400	Enhancers	Fetal Muscle Leg	muscle
8	chr4:7902000-7909200	Enhancers	Fetal Heart	heart
9	chr4:7902000-7909400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:7903400-7911400	Weak transcription	Pancreas	Pancrea
11	chr4:7903400-7911600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:7903600-7915000	Enhancers	Fetal Stomach	stomach
13	chr4:7904200-7909400	Enhancers	Right Atrium	heart
14	chr4:7904400-7909400	Enhancers	NHLF	lung
15	chr4:7904600-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:7904600-7910400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:7904600-7910400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:7904800-7910000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr4:7904800-7910400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:7904800-7911200	Weak transcription	Gastric	stomach
21	chr4:7904800-7912200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:7905000-7911200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:7905200-7907800	Weak transcription	Stomach Mucosa	stomach
24	chr4:7905200-7911200	Weak transcription	Small Intestine	intestine
25	chr4:7905200-7911800	Weak transcription	Aorta	Aorta
26	chr4:7905400-7908200	Enhancers	Brain Anterior Caudate	brain
27	chr4:7905400-7908600	Flanking Active TSS	Osteobl	bone
28	chr4:7905600-7907800	Enhancers	Colon Smooth Muscle	Colon
29	chr4:7905600-7908000	Flanking Active TSS	NHDF-Ad	bronchial
30	chr4:7905600-7908400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:7905600-7908400	Enhancers	Brain Angular Gyrus	brain
32	chr4:7905600-7909200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:7905600-7912400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:7905800-7908000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr4:7905800-7908600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:7905800-7908600	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr4:7905800-7909000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:7905800-7909200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:7905800-7909200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:7905800-7909200	Enhancers	Fetal Kidney	kidney
41	chr4:7905800-7909400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:7905800-7909400	Enhancers	Fetal Thymus	thymus
43	chr4:7906000-7907800	Enhancers	Brain Substantia Nigra	brain
44	chr4:7906000-7908800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr4:7906000-7909000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr4:7906000-7909200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:7906000-7909400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:7906000-7911000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr4:7906000-7914200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr4:7906200-7908000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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