Variant report

Variant	rs28711584
Chromosome Location	chr4:7943639-7943640
allele	A/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	MAX	chr4:7942656-7943891	A549	lung:	n/a	n/a
2	TFAP2A	chr4:7943448-7944294	Hela-S3	cervix:	n/a	chr4:7943615-7943627 chr4:7943615-7943627 chr4:7943615-7943627
3	TFAP2C	chr4:7943160-7944319	Hela-S3	cervix:	n/a	chr4:7943614-7943629

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7900242..7903106-chr4:7943268..7945113,2	MCF-7	breast:
2	chr4:7943385..7945490-chr4:7973996..7976275,2	MCF-7	breast:

Variant related genes	Relation type
AFAP1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12499560	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505812	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2386048	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2386049	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386050	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2386051	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2386053	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2891924	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2891926	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4235266	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4555615	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696685	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696686	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696687	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696824	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4696829	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696830	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696832	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57868040	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58012905	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62290603	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66806187	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7941600-7944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:7941600-7944400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
4	chr4:7942000-7943800	Enhancers	Muscle Satellite Cultured Cells	--
5	chr4:7942000-7943800	Enhancers	Adipose Nuclei	Adipose
6	chr4:7942000-7943800	Enhancers	Pancreas	Pancrea
7	chr4:7942000-7943800	Enhancers	Stomach Mucosa	stomach
8	chr4:7942000-7943800	Enhancers	HepG2	liver
9	chr4:7942000-7943800	Enhancers	HSMM	muscle
10	chr4:7942000-7944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:7942000-7944000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:7942000-7944200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr4:7942000-7944200	Enhancers	Fetal Intestine Large	intestine
14	chr4:7942000-7944200	Enhancers	NHDF-Ad	bronchial
15	chr4:7942000-7944400	Enhancers	Fetal Intestine Small	intestine
16	chr4:7942000-7944600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:7942000-7945200	Enhancers	A549	lung
18	chr4:7942000-7945400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:7942000-7945400	Enhancers	Placenta	Placenta
20	chr4:7942000-7945400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr4:7942000-7946200	Weak transcription	Liver	Liver
22	chr4:7942000-7946400	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:7942000-7946400	Weak transcription	Fetal Stomach	stomach
24	chr4:7942000-7950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr4:7942200-7943800	Enhancers	H9 Cell Line	embryonic stem cell
28	chr4:7942200-7944000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:7942200-7944000	Enhancers	NHEK	skin
30	chr4:7942200-7944800	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:7942200-7947400	Weak transcription	Fetal Brain Male	brain
32	chr4:7942200-7950600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:7942600-7943800	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr4:7942600-7944000	Enhancers	Colonic Mucosa	Colon
35	chr4:7942600-7944200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:7942600-7944200	Enhancers	Duodenum Mucosa	Duodenum
37	chr4:7942600-7944200	Enhancers	NH-A	brain
38	chr4:7942600-7944400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:7942600-7945200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:7942600-7947800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr4:7942800-7943800	Enhancers	Gastric	stomach
42	chr4:7942800-7943800	Enhancers	Lung	lung
43	chr4:7942800-7948000	Weak transcription	Fetal Kidney	kidney
44	chr4:7943000-7944200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr4:7943200-7947400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr4:7943200-7947800	Weak transcription	Ovary	ovary
47	chr4:7943400-7943800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:7943400-7943800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr4:7943400-7946200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:7943600-7944200	Flanking Active TSS	Hela-S3	cervix

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