Variant report

Variant	rs72877460
Chromosome Location	chr3:59521338-59521339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:59521057-59521703	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:59521337-59521387	NHBE	bronchial:	n/a
2	chr3:59521337-59521387	HPAEpiC	pulmonary alveolar:	n/a
3	chr3:59521337-59521387	U87	brain:	n/a
4	chr3:59521337-59521387	PANC-1	pancreas:	n/a
5	chr3:59521337-59521387	HCF	heart:	n/a
6	chr3:59521337-59521387	HIPEpiC	eye:	n/a
7	chr3:59521337-59521387	HAEpiC	amniotic membrane:	n/a
8	chr3:59521337-59521387	AG09309	skin:	n/a
9	chr3:59521337-59521387	NHDF-neo	bronchial:	n/a
10	chr3:59521337-59521387	BJ	skin:	n/a
11	chr3:59521337-59521387	AG04450	lung:	fetal
12	chr3:59521337-59521387	HMEC	breast:	n/a
13	chr3:59521337-59521387	GM06990	blood:	n/a
14	chr3:59521337-59521387	SK-N-SH	brain:	n/a
15	chr3:59521337-59521387	T-47D	breast:	n/a
16	chr3:59521337-59521387	HNPCEpiC	eye:	n/a
17	chr3:59521337-59521387	HUVEC	blood vessel:	n/a
18	chr3:59521337-59521387	ECC-1	luminal epithelium:	n/a
19	chr3:59521337-59521387	Hela-S3	cervix:	n/a
20	chr3:59521337-59521387	HCT-116	colon:	n/a
21	chr3:59521337-59521387	SAEC	small airway:	n/a
22	chr3:59521337-59521387	GM19239	blood:	n/a
23	chr3:59521337-59521387	PrEC	prostate:	n/a
24	chr3:59521337-59521387	ProgFib	skin:	n/a
25	chr3:59521337-59521387	HCM	heart:	n/a
26	chr3:59521337-59521387	HEK293	kidney:	embryo
27	chr3:59521337-59521387	NT2-D1	testis:	n/a
28	chr3:59521337-59521387	GM12878	blood:	n/a
29	chr3:59521337-59521387	GM12891	blood:	n/a
30	chr3:59521337-59521387	NB4	blood:	n/a
31	chr3:59521337-59521387	PFSK-1	brain:	n/a
32	chr3:59521337-59521387	NH-A	brain:	n/a
33	chr3:59521337-59521387	SK-N-SH_RA	brain:	n/a
34	chr3:59521337-59521387	H1-hESC	embryonic stem cell:	embryo
35	chr3:59521337-59521387	AG10803	skin:	n/a
36	chr3:59521337-59521387	Caco-2	colon:	n/a
37	chr3:59521337-59521387	RPTEC	kidney:	n/a
38	chr3:59521337-59521387	SK-N-MC	brain:	n/a
39	chr3:59521337-59521387	AoSMC	blood vessel:	n/a
40	chr3:59521337-59521387	HRE	kidney:	n/a
41	chr3:59521337-59521387	HRCEpiC	kidney:	n/a
42	chr3:59521337-59521387	IMR90	lung:	fetal
43	chr3:59521337-59521387	HEEpiC	esophagus:	n/a
44	chr3:59521337-59521387	ovcar-3	ovarian:	n/a
45	chr3:59521337-59521387	BE2_C	brain:	n/a
46	chr3:59521337-59521387	HepG2	liver:	n/a
47	chr3:59521337-59521387	MCF-7	breast:	n/a
48	chr3:59521337-59521387	A549	lung:	n/a
49	chr3:59521337-59521387	AG09319	gingival:	n/a
50	chr3:59521337-59521387	AG04449	skin:	fetal

No data

Variant related genes	Relation type
ENSG00000241804	TF binding region
ENSG00000241804	CpG island

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs17060878	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060879	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17060883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35500604	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs41502947	0.94[ASN][1000 genomes]
rs58468498	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60650957	0.94[ASN][1000 genomes]
rs61553534	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72875698	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72877405	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72877406	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72877416	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877421	0.94[ASN][1000 genomes]
rs72877424	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72877427	0.94[ASN][1000 genomes]
rs72877429	0.94[ASN][1000 genomes]
rs72877430	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877433	0.94[ASN][1000 genomes]
rs72877434	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877437	0.94[ASN][1000 genomes]
rs72877442	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877443	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877445	0.94[ASN][1000 genomes]
rs72877446	0.94[ASN][1000 genomes]
rs72877447	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877450	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72877453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72877455	0.94[ASN][1000 genomes]
rs72877456	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7356070	0.94[ASN][1000 genomes]
rs7638203	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646357	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311713	0.94[ASN][1000 genomes]
rs9832635	1.00[ASN][1000 genomes]
rs9840238	0.94[ASN][1000 genomes]
rs9848047	0.98[ASN][1000 genomes]
rs9865729	1.00[ASN][1000 genomes]
rs9869699	1.00[ASN][1000 genomes]
rs9870039	1.00[ASN][1000 genomes]
rs9871940	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv876836	chr3:59500394-59664687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59508200-59526200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:59517600-59521800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:59517600-59524800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:59518000-59521800	Weak transcription	Pancreas	Pancrea
5	chr3:59518000-59530800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:59518600-59524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:59520000-59523000	Enhancers	Fetal Heart	heart
8	chr3:59520400-59522400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:59520600-59521800	Enhancers	Colon Smooth Muscle	Colon
10	chr3:59520600-59522400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:59520800-59522800	Enhancers	Osteobl	bone
12	chr3:59520800-59523000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:59521000-59522200	Enhancers	NH-A	brain
14	chr3:59521200-59522400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:59521200-59522800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links