Variant report

Variant	rs28607519
Chromosome Location	chr4:7862389-7862390
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7857940..7860738-chr4:7861450..7863442,2	K562	blood:

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

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

rs_ID	r²[population]
rs11732100	0.88[EUR][1000 genomes]
rs11735005	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13130704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17770213	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17770321	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17832709	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28375300	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28417050	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28437157	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28438948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28494514	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28544299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558196	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28568794	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28600706	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622214	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28694545	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28766602	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34033399	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34310670	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55844411	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56220381	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56229515	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56411722	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61742221	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62289320	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289333	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289335	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62289336	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289337	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289338	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289339	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289340	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62289359	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62290561	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62290571	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62290573	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290574	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290579	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6814219	0.85[EUR][1000 genomes]
rs6814887	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815298	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829680	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6838073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6850654	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6855532	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73210862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73210866	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214041	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73214042	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7378072	0.85[EUR][1000 genomes]
rs7663026	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7680747	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687428	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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
rs28607519	AFAP1	cis	Esophagus Mucosa	GTEx
rs28607519	AFAP1	cis	Whole Blood	GTEx
rs28607519	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7830400-7862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:7830600-7862400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:7843600-7863000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:7845000-7863200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:7855200-7863400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:7855600-7863200	Weak transcription	Hela-S3	cervix
9	chr4:7855800-7862400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:7856200-7872800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:7856400-7865600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:7856400-7865800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:7856600-7862600	Genic enhancers	A549	lung
14	chr4:7856600-7863200	Weak transcription	Fetal Kidney	kidney
15	chr4:7857000-7862400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:7857200-7863200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:7857200-7864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:7857600-7873000	Weak transcription	Colonic Mucosa	Colon
19	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
20	chr4:7858400-7862400	Weak transcription	Esophagus	oesophagus
21	chr4:7858600-7862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:7859000-7865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr4:7859400-7863000	Weak transcription	Adipose Nuclei	Adipose
24	chr4:7859400-7863600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:7859400-7865600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:7859400-7865600	Genic enhancers	Osteobl	bone
27	chr4:7859600-7862400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:7859600-7862400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:7859600-7869000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:7859600-7869400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:7859800-7865600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:7859800-7865600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:7859800-7865600	Weak transcription	Brain Angular Gyrus	brain
34	chr4:7859800-7865600	Weak transcription	Stomach Mucosa	stomach
35	chr4:7859800-7872600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:7860000-7862400	Weak transcription	Brain Germinal Matrix	brain
37	chr4:7860000-7864800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:7860000-7864800	Genic enhancers	HSMMtube	muscle
39	chr4:7860000-7865600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:7860000-7865600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:7860200-7867600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:7860400-7862400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:7860400-7862400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr4:7860400-7862600	Weak transcription	Fetal Lung	lung
45	chr4:7860400-7865600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:7860400-7870200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr4:7860600-7862400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:7860600-7862600	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr4:7860600-7862800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:7860600-7862800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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