Variant report

Variant	rs28892906
Chromosome Location	chr4:7875265-7875266
allele	C/T
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	POLR2A	chr4:7875207-7875967	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6814219	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7378072	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28892906	AFAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs28892906	AFAP1	cis	Whole Blood	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7857800-7896400	Weak transcription	Spleen	Spleen
2	chr4:7865400-7875800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:7866000-7875400	Weak transcription	Stomach Mucosa	stomach
4	chr4:7866000-7877600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:7866000-7877800	Weak transcription	HepG2	liver
6	chr4:7866000-7882400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:7866000-7885600	Weak transcription	Esophagus	oesophagus
8	chr4:7869200-7880800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:7869600-7877600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:7869800-7878000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:7870400-7876800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:7870400-7879200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:7870400-7882400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:7870600-7877200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:7870600-7877200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:7870600-7877600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:7870600-7878000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:7870600-7878000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:7873000-7875800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:7873400-7875400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:7873400-7875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:7873400-7875600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr4:7873400-7875800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:7873400-7876000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:7873400-7877200	Weak transcription	Primary T cells from cord blood	blood
26	chr4:7873400-7878800	Weak transcription	Fetal Intestine Small	intestine
27	chr4:7873400-7879000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:7873400-7880000	Weak transcription	Lung	lung
29	chr4:7873400-7883000	Weak transcription	Right Ventricle	heart
30	chr4:7873600-7878000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:7873600-7878200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:7873600-7894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:7873800-7875400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:7873800-7875600	Enhancers	NHEK	skin
35	chr4:7873800-7878200	Weak transcription	Fetal Intestine Large	intestine
36	chr4:7874000-7876000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:7874200-7877800	Weak transcription	Ovary	ovary
38	chr4:7874400-7875400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:7874400-7875600	Enhancers	HSMMtube	muscle
40	chr4:7874400-7877800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:7874400-7878000	Weak transcription	Fetal Kidney	kidney
42	chr4:7874400-7878000	Weak transcription	Left Ventricle	heart
43	chr4:7874400-7878200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:7874400-7878600	Weak transcription	Fetal Brain Female	brain
45	chr4:7874400-7880200	Weak transcription	Gastric	stomach
46	chr4:7874400-7880200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:7874400-7880800	Weak transcription	Pancreas	Pancrea
48	chr4:7874600-7875400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:7874600-7875400	Weak transcription	Fetal Lung	lung
50	chr4:7874600-7875400	Weak transcription	A549	lung

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