Variant report

Variant	rs28376859
Chromosome Location	chr4:7868217-7868218
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr4:7867908-7868375	IMR90	lung:	n/a	chr4:7868284-7868297 chr4:7868267-7868280

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10938695	0.82[ASN][1000 genomes]
rs13115283	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28410206	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28500712	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28503942	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28572044	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549363	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59283470	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59521811	0.81[ASN][1000 genomes]
rs62289323	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62289332	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831381	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6845653	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7375284	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7376648	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7378106	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28376859	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:105 , 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	chr4:7857600-7873000	Weak transcription	Colonic Mucosa	Colon
5	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
6	chr4:7859600-7869000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:7859600-7869400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:7859800-7872600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:7860400-7870200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:7860800-7869000	Weak transcription	Aorta	Aorta
11	chr4:7860800-7872800	Weak transcription	Right Ventricle	heart
12	chr4:7861200-7872800	Weak transcription	Psoas Muscle	Psoas
13	chr4:7862600-7870000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:7862800-7868600	Weak transcription	Left Ventricle	heart
15	chr4:7863600-7868400	Weak transcription	Placenta	Placenta
16	chr4:7863600-7869000	Weak transcription	Adipose Nuclei	Adipose
17	chr4:7863600-7871000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:7863800-7869000	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:7863800-7869000	Weak transcription	Fetal Brain Female	brain
20	chr4:7863800-7869000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr4:7863800-7872800	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:7864800-7873000	Weak transcription	Primary T cells from cord blood	blood
23	chr4:7865200-7872200	Weak transcription	Right Atrium	heart
24	chr4:7865400-7868400	Weak transcription	Brain Germinal Matrix	brain
25	chr4:7865400-7869000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:7865400-7872600	Weak transcription	Fetal Heart	heart
27	chr4:7865400-7875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:7865800-7869200	Weak transcription	Brain Anterior Caudate	brain
29	chr4:7865800-7870000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:7865800-7871400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:7865800-7872000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:7865800-7872800	Strong transcription	Fetal Stomach	stomach
33	chr4:7866000-7868600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:7866000-7868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:7866000-7868600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:7866000-7868600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:7866000-7869000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:7866000-7869000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr4:7866000-7869000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:7866000-7869000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr4:7866000-7869000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:7866000-7869000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:7866000-7869000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:7866000-7869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:7866000-7869000	Weak transcription	Ovary	ovary
46	chr4:7866000-7869000	Weak transcription	HMEC	breast
47	chr4:7866000-7869000	Weak transcription	NHEK	skin
48	chr4:7866000-7869200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:7866000-7869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:7866000-7869200	Weak transcription	Hela-S3	cervix

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