Variant report

Variant	rs28446696
Chromosome Location	chr4:7942027-7942028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr4:7941282-7942050	SK-N-SH	brain:	n/a	n/a
2	CHD1	chr4:7938516-7942221	IMR90	lung:	n/a	n/a
3	POLR2A	chr4:7939500-7942061	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr4:7941125-7942031	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr4:7941216-7942047	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr4:7939516-7942080	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:7941205-7942079	PFSK-1	brain:	n/a	n/a
8	MAZ	chr4:7939417-7942102	IMR90	lung:	n/a	chr4:7940793-7940802
9	POLR2A	chr4:7940248-7942132	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr4:7941184-7942061	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:7940383-7942109	H1-neurons	neurons:	n/a	n/a
12	ZBTB7A	chr4:7940291-7942133	ECC-1	luminal epithelium:	n/a	n/a
13	ZBTB7A	chr4:7941635-7942053	ECC-1	luminal epithelium:	n/a	n/a
14	MXI1	chr4:7939421-7942036	IMR90	lung:	n/a	n/a
15	POLR2A	chr4:7941128-7942066	MCF-7	breast:	n/a	n/a
16	POLR2A	chr4:7941247-7942085	H1-hESC	embryonic stem cell:	n/a	n/a
17	TCF12	chr4:7941257-7942116	ECC-1	luminal epithelium:	n/a	n/a
18	REST	chr4:7940533-7942237	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr4:7941176-7942048	MCF-7	breast:	n/a	n/a
20	POLR2A	chr4:7941289-7942054	SK-N-SH	brain:	n/a	n/a
21	MXI1	chr4:7939452-7942147	SK-N-SH	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:7942020-7942070	A549	lung:	n/a
2	chr4:7942020-7942070	HRE	kidney:	n/a
3	chr4:7942020-7942070	ProgFib	skin:	n/a
4	chr4:7942020-7942070	H1-hESC	embryonic stem cell:	embryo
5	chr4:7942020-7942070	HL-60	blood:	n/a
6	chr4:7942020-7942070	SK-N-MC	brain:	n/a
7	chr4:7942020-7942070	HPAEpiC	pulmonary alveolar:	n/a
8	chr4:7942020-7942070	Hela-S3	cervix:	n/a
9	chr4:7942020-7942070	AG09309	skin:	n/a
10	chr4:7942020-7942070	GM12878	blood:	n/a
11	chr4:7942020-7942070	HUVEC	blood vessel:	n/a
12	chr4:7942020-7942070	AG04449	skin:	fetal
13	chr4:7942020-7942070	HCF	heart:	n/a
14	chr4:7942020-7942070	HCPEpiC	choroid plexus:	n/a
15	chr4:7942020-7942070	T-47D	breast:	n/a
16	chr4:7942020-7942070	K562	blood:	n/a
17	chr4:7942020-7942070	GM12891	blood:	n/a
18	chr4:7942020-7942070	LNCaP	prostate:	n/a
19	chr4:7942020-7942070	RPTEC	kidney:	n/a
20	chr4:7942020-7942070	HNPCEpiC	eye:	n/a
21	chr4:7942020-7942070	AG09319	gingival:	n/a
22	chr4:7942020-7942070	U87	brain:	n/a
23	chr4:7942020-7942070	PFSK-1	brain:	n/a
24	chr4:7942020-7942070	HAEpiC	amniotic membrane:	n/a
25	chr4:7942020-7942070	AG04450	lung:	fetal
26	chr4:7942020-7942070	NB4	blood:	n/a
27	chr4:7942020-7942070	HRPEpiC	eye:	n/a
28	chr4:7942020-7942070	NT2-D1	testis:	n/a
29	chr4:7942020-7942070	HRCEpiC	kidney:	n/a
30	chr4:7942020-7942070	AoSMC	blood vessel:	n/a
31	chr4:7942020-7942070	MCF10A-Er-Src	breast:	n/a
32	chr4:7942020-7942070	SKMC	muscle:	n/a
33	chr4:7942020-7942070	ECC-1	luminal epithelium:	n/a
34	chr4:7942020-7942070	HEEpiC	esophagus:	n/a
35	chr4:7942020-7942070	HepG2	liver:	n/a
36	chr4:7942020-7942070	AG10803	skin:	n/a
37	chr4:7942020-7942070	IMR90	lung:	fetal
38	chr4:7942020-7942070	PrEC	prostate:	n/a
39	chr4:7942020-7942070	HEK293	kidney:	embryo
40	chr4:7942020-7942070	NHBE	bronchial:	n/a
41	chr4:7942020-7942070	GM12892	blood:	n/a
42	chr4:7942020-7942070	Caco-2	colon:	n/a
43	chr4:7942020-7942070	GM06990	blood:	n/a
44	chr4:7942020-7942070	Jurkat	blood:	n/a
45	chr4:7942020-7942070	SAEC	small airway:	n/a
46	chr4:7942020-7942070	ovcar-3	ovarian:	n/a
47	chr4:7942020-7942070	NH-A	brain:	n/a
48	chr4:7942020-7942070	BJ	skin:	n/a
49	chr4:7942020-7942070	HIPEpiC	eye:	n/a
50	chr4:7942020-7942070	PANC-1	pancreas:	n/a

No data

Variant related genes	Relation type
AFAP1	TF binding region
AFAP1	CpG island

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12696835	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344223	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2385912	0.84[EUR][1000 genomes]
rs2385914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34072960	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34740645	0.83[AMR][1000 genomes]
rs58349148	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60272249	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66479458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6840305	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846757	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7669433	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7669645	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695142	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695170	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7698368	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9993085	0.88[EUR][1000 genomes];0.87[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	esv3370778	chr4:7940277-7942825	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7940200-7942200	Active TSS	Fetal Lung	lung
2	chr4:7940400-7942200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:7940400-7942200	Active TSS	Brain Angular Gyrus	brain
4	chr4:7941000-7942200	Active TSS	Brain Cingulate Gyrus	brain
5	chr4:7941200-7942200	Active TSS	Fetal Brain Female	brain
6	chr4:7941400-7942200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:7941600-7942600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:7941600-7942800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:7941600-7943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:7941600-7944000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:7941600-7944400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
13	chr4:7941800-7942200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:7941800-7942200	Enhancers	Fetal Brain Male	brain
15	chr4:7941800-7942200	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr4:7941800-7943600	Enhancers	Fetal Heart	heart
17	chr4:7942000-7942200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:7942000-7942200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:7942000-7942200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:7942000-7942200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr4:7942000-7942200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:7942000-7942200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr4:7942000-7942200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:7942000-7942200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:7942000-7942200	Enhancers	Colonic Mucosa	Colon
26	chr4:7942000-7942200	Enhancers	Duodenum Mucosa	Duodenum
27	chr4:7942000-7942200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:7942000-7942200	Active TSS	Fetal Kidney	kidney
29	chr4:7942000-7942200	Enhancers	Fetal Muscle Leg	muscle
30	chr4:7942000-7942200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr4:7942000-7942200	Enhancers	Right Ventricle	heart
32	chr4:7942000-7942200	Active TSS	HUVEC	blood vessel
33	chr4:7942000-7942200	Enhancers	NH-A	brain
34	chr4:7942000-7942200	Weak transcription	NHEK	skin
35	chr4:7942000-7942400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:7942000-7942600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:7942000-7942600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:7942000-7942600	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr4:7942000-7942600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:7942000-7942600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:7942000-7942600	Weak transcription	Spleen	Spleen
42	chr4:7942000-7942800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr4:7942000-7942800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:7942000-7942800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr4:7942000-7942800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr4:7942000-7942800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr4:7942000-7942800	Weak transcription	Gastric	stomach
48	chr4:7942000-7942800	Weak transcription	Lung	lung
49	chr4:7942000-7942800	Weak transcription	Ovary	ovary
50	chr4:7942000-7942800	Enhancers	Hela-S3	cervix

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