Variant report

Variant	rs28406288
Chromosome Location	chr4:7802227-7802228
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:7802192-7802242	NT2-D1	testis:	n/a
2	chr4:7802192-7802242	PrEC	prostate:	n/a
3	chr4:7802192-7802242	T-47D	breast:	n/a
4	chr4:7802192-7802242	BJ	skin:	n/a
5	chr4:7802192-7802242	PFSK-1	brain:	n/a
6	chr4:7802192-7802242	ProgFib	skin:	n/a
7	chr4:7802192-7802242	Jurkat	blood:	n/a
8	chr4:7802192-7802242	HIPEpiC	eye:	n/a
9	chr4:7802192-7802242	GM12878	blood:	n/a
10	chr4:7802192-7802242	HCM	heart:	n/a
11	chr4:7802192-7802242	ECC-1	luminal epithelium:	n/a
12	chr4:7802192-7802242	HMEC	breast:	n/a
13	chr4:7802192-7802242	NH-A	brain:	n/a
14	chr4:7802192-7802242	AG10803	skin:	n/a
15	chr4:7802192-7802242	NB4	blood:	n/a
16	chr4:7802192-7802242	AG04450	lung:	fetal
17	chr4:7802192-7802242	HRE	kidney:	n/a
18	chr4:7802192-7802242	H1-hESC	embryonic stem cell:	embryo
19	chr4:7802192-7802242	AG09319	gingival:	n/a
20	chr4:7802192-7802242	SK-N-MC	brain:	n/a
21	chr4:7802192-7802242	SAEC	small airway:	n/a
22	chr4:7802192-7802242	HCT-116	colon:	n/a
23	chr4:7802192-7802242	HEEpiC	esophagus:	n/a
24	chr4:7802192-7802242	HRPEpiC	eye:	n/a
25	chr4:7802192-7802242	K562	blood:	n/a
26	chr4:7802192-7802242	AoSMC	blood vessel:	n/a
27	chr4:7802192-7802242	IMR90	lung:	fetal
28	chr4:7802192-7802242	Caco-2	colon:	n/a
29	chr4:7802192-7802242	NHDF-neo	bronchial:	n/a
30	chr4:7802192-7802242	PANC-1	pancreas:	n/a
31	chr4:7802192-7802242	GM19239	blood:	n/a
32	chr4:7802192-7802242	A549	lung:	n/a
33	chr4:7802192-7802242	U87	brain:	n/a
34	chr4:7802192-7802242	GM06990	blood:	n/a
35	chr4:7802192-7802242	HEK293	kidney:	embryo
36	chr4:7802192-7802242	HepG2	liver:	n/a
37	chr4:7802192-7802242	NHBE	bronchial:	n/a
38	chr4:7802192-7802242	HCF	heart:	n/a
39	chr4:7802192-7802242	GM12892	blood:	n/a
40	chr4:7802192-7802242	SKMC	muscle:	n/a
41	chr4:7802192-7802242	Hela-S3	cervix:	n/a
42	chr4:7802192-7802242	HUVEC	blood vessel:	n/a
43	chr4:7802192-7802242	HRCEpiC	kidney:	n/a
44	chr4:7802192-7802242	AG04449	skin:	fetal
45	chr4:7802192-7802242	HL-60	blood:	n/a
46	chr4:7802192-7802242	BE2_C	brain:	n/a
47	chr4:7802192-7802242	GM12891	blood:	n/a
48	chr4:7802192-7802242	SK-N-SH_RA	brain:	n/a
49	chr4:7802192-7802242	ovcar-3	ovarian:	n/a
50	chr4:7802192-7802242	HAEpiC	amniotic membrane:	n/a

No data

Variant related genes	Relation type
AFAP1	CpG island

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10000569	0.83[ASN][1000 genomes]
rs10004558	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10022249	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025396	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031989	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10050114	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10155361	0.86[AMR][1000 genomes]
rs10937858	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10937860	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10937862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11944501	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501412	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503512	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508657	0.85[AMR][1000 genomes]
rs12511825	0.87[EUR][1000 genomes]
rs16841116	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841207	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429656	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726367	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28735524	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28759100	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689857	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689858	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4689861	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6856818	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73206599	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73208810	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356232	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[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	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
2	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
5	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
7	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:7785800-7803800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:7787000-7829400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr4:7789200-7806600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:7790800-7803600	Strong transcription	HSMM	muscle
13	chr4:7791000-7806600	Weak transcription	Psoas Muscle	Psoas
14	chr4:7791000-7829400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:7791400-7806600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:7792200-7803200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:7792600-7802800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:7792600-7803400	Strong transcription	A549	lung
19	chr4:7792800-7803000	Strong transcription	HSMMtube	muscle
20	chr4:7793200-7803800	Strong transcription	NH-A	brain
21	chr4:7794400-7803600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:7794800-7803400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:7795600-7803800	Weak transcription	Fetal Kidney	kidney
24	chr4:7795800-7803800	Weak transcription	Fetal Heart	heart
25	chr4:7796000-7803400	Strong transcription	HUVEC	blood vessel
26	chr4:7796600-7803400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:7796800-7804200	Strong transcription	NHEK	skin
28	chr4:7797000-7807000	Weak transcription	Liver	Liver
29	chr4:7797200-7803000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:7797200-7803800	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr4:7797600-7802400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr4:7797600-7802800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr4:7797600-7803000	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:7797600-7803200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:7797600-7803200	Strong transcription	Fetal Stomach	stomach
36	chr4:7797800-7802800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:7797800-7802800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:7797800-7802800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr4:7797800-7802800	Strong transcription	Placenta	Placenta
40	chr4:7797800-7803000	Strong transcription	NHLF	lung
41	chr4:7797800-7803200	Strong transcription	NHDF-Ad	bronchial
42	chr4:7797800-7803400	Strong transcription	Fetal Intestine Large	intestine
43	chr4:7797800-7803600	Strong transcription	Fetal Muscle Leg	muscle
44	chr4:7798200-7807200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:7798400-7803000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr4:7798600-7803000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:7798600-7803000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:7798800-7802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr4:7798800-7802600	Strong transcription	Adipose Nuclei	Adipose
50	chr4:7798800-7802600	Strong transcription	Fetal Lung	lung

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