Variant report

Variant	rs28505096
Chromosome Location	chr4:48083396-48083397
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	GATA3	chr4:48082925-48083765	SK-N-SH	brain:	n/a	chr4:48083348-48083359 chr4:48083370-48083381 chr4:48083355-48083363 chr4:48083314-48083330
2	FOSL2	chr4:48083220-48083620	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr4:48082979-48083764	SK-N-SH	brain:	n/a	chr4:48083348-48083359 chr4:48083370-48083381 chr4:48083355-48083363 chr4:48083314-48083330
4	TCF12	chr4:48083108-48083703	SK-N-SH	brain:	n/a	n/a
5	JUND	chr4:48083211-48083594	Hela-S3	cervix:	n/a	n/a
6	RCOR1	chr4:48083236-48083595	Hela-S3	cervix:	n/a	n/a
7	EP300	chr4:48083208-48083539	Hela-S3	cervix:	n/a	n/a
8	GATA2	chr4:48083182-48083874	HUVEC	blood vessel:	n/a	chr4:48083348-48083359 chr4:48083370-48083381 chr4:48083355-48083363 chr4:48083314-48083330
9	JUN	chr4:48083223-48083758	Hela-S3	cervix:	n/a	n/a
10	EP300	chr4:48083150-48083578	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr4:48083224-48083552	SK-N-SH	brain:	n/a	n/a
12	RFX5	chr4:48083243-48083568	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr4:48083128-48083524	A549	lung:	n/a	chr4:48083348-48083359 chr4:48083370-48083381 chr4:48083355-48083363 chr4:48083314-48083330
14	CEBPB	chr4:48083203-48083513	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:48083394-48083444	NH-A	brain:	n/a
2	chr4:48083394-48083444	ProgFib	skin:	n/a
3	chr4:48083394-48083444	HRPEpiC	eye:	n/a
4	chr4:48083394-48083444	LNCaP	prostate:	n/a
5	chr4:48083394-48083444	HUVEC	blood vessel:	n/a
6	chr4:48083394-48083444	A549	lung:	n/a
7	chr4:48083394-48083444	HIPEpiC	eye:	n/a
8	chr4:48083394-48083444	BJ	skin:	n/a
9	chr4:48083394-48083444	RPTEC	kidney:	n/a
10	chr4:48083394-48083444	NT2-D1	testis:	n/a
11	chr4:48083394-48083444	AG10803	skin:	n/a
12	chr4:48083394-48083444	HRE	kidney:	n/a
13	chr4:48083394-48083444	Caco-2	colon:	n/a
14	chr4:48083394-48083444	HL-60	blood:	n/a
15	chr4:48083394-48083444	CMK	blood:	n/a
16	chr4:48083394-48083444	HRCEpiC	kidney:	n/a
17	chr4:48083394-48083444	GM12892	blood:	n/a
18	chr4:48083394-48083444	AG09309	skin:	n/a
19	chr4:48083394-48083444	HepG2	liver:	n/a
20	chr4:48083394-48083444	AG04449	skin:	fetal
21	chr4:48083394-48083444	ECC-1	luminal epithelium:	n/a
22	chr4:48083394-48083444	HCF	heart:	n/a
23	chr4:48083394-48083444	PFSK-1	brain:	n/a
24	chr4:48083394-48083444	GM06990	blood:	n/a
25	chr4:48083394-48083444	SKMC	muscle:	n/a
26	chr4:48083394-48083444	SK-N-SH	brain:	n/a
27	chr4:48083394-48083444	Jurkat	blood:	n/a
28	chr4:48083394-48083444	HEK293	kidney:	embryo
29	chr4:48083394-48083444	HPAEpiC	pulmonary alveolar:	n/a
30	chr4:48083394-48083444	SK-N-MC	brain:	n/a
31	chr4:48083394-48083444	AoSMC	blood vessel:	n/a
32	chr4:48083394-48083444	AG04450	lung:	fetal
33	chr4:48083394-48083444	HCT-116	colon:	n/a
34	chr4:48083394-48083444	K562	blood:	n/a
35	chr4:48083394-48083444	Hela-S3	cervix:	n/a
36	chr4:48083394-48083444	HEEpiC	esophagus:	n/a
37	chr4:48083394-48083444	SK-N-SH_RA	brain:	n/a
38	chr4:48083394-48083444	ovcar-3	ovarian:	n/a
39	chr4:48083394-48083444	BE2_C	brain:	n/a
40	chr4:48083394-48083444	HMEC	breast:	n/a
41	chr4:48083394-48083444	GM12878	blood:	n/a
42	chr4:48083394-48083444	HNPCEpiC	eye:	n/a
43	chr4:48083394-48083444	GM19239	blood:	n/a
44	chr4:48083394-48083444	SAEC	small airway:	n/a
45	chr4:48083394-48083444	U87	brain:	n/a
46	chr4:48083394-48083444	PANC-1	pancreas:	n/a
47	chr4:48083394-48083444	T-47D	breast:	n/a
48	chr4:48083394-48083444	Hepatocyte	liver:	n/a
49	chr4:48083394-48083444	NB4	blood:	n/a
50	chr4:48083394-48083444	IMR90	lung:	fetal

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

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1018199	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046695	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722304	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11724102	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11724347	1.00[ASN][1000 genomes]
rs11737047	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108221	1.00[ASN][1000 genomes]
rs1507924	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352587	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352588	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34184567	1.00[ASN][1000 genomes]
rs36082349	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55781011	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814131	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832282	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837702	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6844476	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73151629	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906486	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr4:48069800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
4	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:48076600-48092400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:48079000-48084600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:48079000-48087400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:48080600-48084600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:48080600-48084600	Enhancers	Hela-S3	cervix
11	chr4:48080600-48085200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:48081400-48083400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr4:48081400-48083400	Enhancers	NHEK	skin
14	chr4:48081600-48094200	Weak transcription	Pancreas	Pancrea
15	chr4:48081800-48083400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:48081800-48083800	Weak transcription	Placenta	Placenta
17	chr4:48082000-48083400	Genic enhancers	Primary T cells from cord blood	blood
18	chr4:48082400-48085200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr4:48082400-48088400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:48082600-48083800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:48082600-48083800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:48082600-48084000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:48082600-48084000	Enhancers	NH-A	brain
24	chr4:48082600-48084400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:48082600-48085200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:48082600-48086200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr4:48082600-48088000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:48082800-48083400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:48082800-48083800	Weak transcription	HSMM	muscle
30	chr4:48082800-48084400	Enhancers	HUVEC	blood vessel
31	chr4:48082800-48088200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:48082800-48088200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:48083000-48083400	Weak transcription	A549	lung
34	chr4:48083000-48098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:48083000-48098200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links