Variant report

Variant	rs4552460
Chromosome Location	chr4:7863618-7863619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17770936	0.81[CEU][hapmap]
rs28379782	0.93[ASN][1000 genomes]
rs28393652	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28418478	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28451112	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28468456	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28508479	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28612887	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28621561	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28638094	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28649910	0.87[EUR][1000 genomes]
rs28657375	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28657625	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28662492	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28728216	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28861809	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4234834	0.80[AMR][1000 genomes]
rs4377592	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4383619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4388087	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4404542	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4413405	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4473655	0.91[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4496581	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4496582	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4605652	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4623000	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6838291	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs7376416	0.93[ASN][1000 genomes]
rs7440527	1.00[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4552460	AFAP1	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7848000-7872200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:7852600-7873600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:7856200-7872800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:7856400-7865600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr4:7856400-7865800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr4:7857200-7864800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr4:7857600-7873000	Weak transcription	Colonic Mucosa	Colon
8	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
9	chr4:7859000-7865600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr4:7859400-7865600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:7859400-7865600	Genic enhancers	Osteobl	bone
12	chr4:7859600-7869000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:7859600-7869400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr4:7859800-7865600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:7859800-7865600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:7859800-7865600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:7859800-7865600	Weak transcription	Stomach Mucosa	stomach
18	chr4:7859800-7872600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:7860000-7864800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:7860000-7864800	Genic enhancers	HSMMtube	muscle
21	chr4:7860000-7865600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:7860000-7865600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:7860200-7867600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:7860400-7865600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:7860400-7870200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:7860600-7865600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr4:7860800-7865600	Weak transcription	Gastric	stomach
28	chr4:7860800-7865600	Weak transcription	Lung	lung
29	chr4:7860800-7865600	Weak transcription	Pancreas	Pancrea
30	chr4:7860800-7869000	Weak transcription	Aorta	Aorta
31	chr4:7860800-7872800	Weak transcription	Right Ventricle	heart
32	chr4:7861200-7872800	Weak transcription	Psoas Muscle	Psoas
33	chr4:7861400-7863800	Genic enhancers	Fetal Muscle Leg	muscle
34	chr4:7861400-7865600	Weak transcription	HepG2	liver
35	chr4:7862000-7863800	Enhancers	Fetal Brain Female	brain
36	chr4:7862000-7865200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr4:7862000-7865600	Genic enhancers	HSMM	muscle
38	chr4:7862200-7863800	Enhancers	Colon Smooth Muscle	Colon
39	chr4:7862200-7863800	Strong transcription	Fetal Intestine Large	intestine
40	chr4:7862200-7863800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr4:7862200-7864000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:7862200-7865000	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:7862200-7865200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:7862200-7865400	Enhancers	Fetal Brain Male	brain
45	chr4:7862400-7864000	Enhancers	HMEC	breast
46	chr4:7862400-7864200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:7862400-7864600	Enhancers	Brain Germinal Matrix	brain
48	chr4:7862400-7865400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr4:7862600-7863800	Flanking Active TSS	A549	lung
50	chr4:7862600-7864600	Enhancers	NHDF-Ad	bronchial

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