Variant report

Variant	rs28378297
Chromosome Location	chr3:42947483-42947484
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:42947440-42947590	AG09309	skin:	n/a	n/a
2	YY1	chr3:42947464-42947986	SK-N-SH_RA	brain:	n/a	chr3:42947472-42947483

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42947481-42947531	HCF	heart:	n/a
2	chr3:42947481-42947531	ovcar-3	ovarian:	n/a
3	chr3:42947481-42947531	HMEC	breast:	n/a
4	chr3:42947481-42947531	PFSK-1	brain:	n/a
5	chr3:42947481-42947531	AG10803	skin:	n/a
6	chr3:42947481-42947531	T-47D	breast:	n/a
7	chr3:42947481-42947531	ProgFib	skin:	n/a
8	chr3:42947481-42947531	AoSMC	blood vessel:	n/a
9	chr3:42947481-42947531	K562	blood:	n/a
10	chr3:42947481-42947531	U87	brain:	n/a
11	chr3:42947481-42947531	GM12892	blood:	n/a
12	chr3:42947481-42947531	SAEC	small airway:	n/a
13	chr3:42947481-42947531	SK-N-SH_RA	brain:	n/a
14	chr3:42947481-42947531	LNCaP	prostate:	n/a
15	chr3:42947481-42947531	GM12891	blood:	n/a
16	chr3:42947481-42947531	IMR90	lung:	fetal
17	chr3:42947481-42947531	HepG2	liver:	n/a
18	chr3:42947481-42947531	HCPEpiC	choroid plexus:	n/a
19	chr3:42947481-42947531	NHBE	bronchial:	n/a
20	chr3:42947481-42947531	HEEpiC	esophagus:	n/a
21	chr3:42947481-42947531	BE2_C	brain:	n/a
22	chr3:42947481-42947531	H1-hESC	embryonic stem cell:	embryo
23	chr3:42947481-42947531	Hepatocyte	liver:	n/a
24	chr3:42947481-42947531	SK-N-SH	brain:	n/a
25	chr3:42947481-42947531	HUVEC	blood vessel:	n/a
26	chr3:42947481-42947531	NT2-D1	testis:	n/a
27	chr3:42947481-42947531	GM12878	blood:	n/a
28	chr3:42947481-42947531	HAEpiC	amniotic membrane:	n/a
29	chr3:42947481-42947531	HRPEpiC	eye:	n/a
30	chr3:42947481-42947531	RPTEC	kidney:	n/a
31	chr3:42947481-42947531	ECC-1	luminal epithelium:	n/a
32	chr3:42947481-42947531	HIPEpiC	eye:	n/a
33	chr3:42947481-42947531	AG04450	lung:	fetal
34	chr3:42947481-42947531	AG09319	gingival:	n/a
35	chr3:42947481-42947531	HCM	heart:	n/a
36	chr3:42947481-42947531	GM06990	blood:	n/a
37	chr3:42947481-42947531	HCT-116	colon:	n/a
38	chr3:42947481-42947531	NB4	blood:	n/a
39	chr3:42947481-42947531	MCF10A-Er-Src	breast:	n/a
40	chr3:42947481-42947531	PrEC	prostate:	n/a
41	chr3:42947481-42947531	HPAEpiC	pulmonary alveolar:	n/a
42	chr3:42947481-42947531	MCF-7	breast:	n/a
43	chr3:42947481-42947531	SK-N-MC	brain:	n/a
44	chr3:42947481-42947531	SKMC	muscle:	n/a
45	chr3:42947481-42947531	NH-A	brain:	n/a
46	chr3:42947481-42947531	HEK293	kidney:	embryo
47	chr3:42947481-42947531	HL-60	blood:	n/a
48	chr3:42947481-42947531	HRE	kidney:	n/a
49	chr3:42947481-42947531	Hela-S3	cervix:	n/a
50	chr3:42947481-42947531	PANC-1	pancreas:	n/a

No data

Variant related genes	Relation type
ZNF662	TF binding region
ZNF662	CpG island

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10470680	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129987	0.82[EUR][1000 genomes]
rs11129988	0.82[EUR][1000 genomes]
rs1346415	0.80[EUR][1000 genomes]
rs1392319	1.00[ASN][1000 genomes]
rs1403525	1.00[ASN][1000 genomes]
rs17074894	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238972	1.00[ASN][1000 genomes]
rs1816227	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601753	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	1.00[ASN][1000 genomes]
rs28673478	1.00[ASN][1000 genomes]
rs3915020	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489117	1.00[ASN][1000 genomes]
rs526511	0.80[EUR][1000 genomes]
rs530842	1.00[ASN][1000 genomes]
rs534284	1.00[ASN][1000 genomes]
rs542394	0.81[EUR][1000 genomes]
rs545023	0.81[EUR][1000 genomes]
rs551658	1.00[ASN][1000 genomes]
rs604393	1.00[ASN][1000 genomes]
rs60616619	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61004728	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs62248962	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249007	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249008	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249009	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249011	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249013	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249014	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.81[EUR][1000 genomes]
rs62249016	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	1.00[ASN][1000 genomes]
rs638602	0.80[EUR][1000 genomes]
rs651899	1.00[ASN][1000 genomes]
rs6763762	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773223	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775999	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678310	1.00[ASN][1000 genomes]
rs6798412	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798520	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs680967	1.00[ASN][1000 genomes]
rs681341	1.00[ASN][1000 genomes]
rs6865	1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs73087348	1.00[ASN][1000 genomes]
rs735320	1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641452	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644923	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834183	0.80[EUR][1000 genomes]
rs834579	0.82[EUR][1000 genomes]
rs834584	0.80[EUR][1000 genomes]
rs834699	0.80[EUR][1000 genomes]
rs9311330	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311331	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808932	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815609	1.00[ASN][1000 genomes]
rs9816391	1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	1.00[ASN][1000 genomes]
rs9832875	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9833284	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837761	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	1.00[ASN][1000 genomes]
rs9852930	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858270	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862469	1.00[ASN][1000 genomes]
rs9870478	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	nsv3783	chr3:42926223-42970597	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42942600-42947600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:42946600-42948400	Active TSS	Brain Anterior Caudate	brain
3	chr3:42946800-42947600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr3:42946800-42948800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:42947000-42947600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:42947000-42947600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr3:42947000-42947600	Flanking Active TSS	Stomach Mucosa	stomach
8	chr3:42947000-42947800	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:42947000-42947800	Active TSS	Right Ventricle	heart
10	chr3:42947000-42948000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:42947000-42948200	Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr3:42947000-42948200	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr3:42947000-42948200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:42947000-42948200	Active TSS	Rectal Smooth Muscle	rectum
15	chr3:42947000-42948200	Active TSS	Right Atrium	heart
16	chr3:42947000-42948400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:42947000-42948400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr3:42947000-42948800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:42947200-42947600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
20	chr3:42947200-42947600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
21	chr3:42947200-42947600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:42947200-42947600	Flanking Active TSS	Fetal Brain Male	brain
23	chr3:42947200-42947600	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr3:42947200-42947600	Flanking Active TSS	Fetal Stomach	stomach
25	chr3:42947200-42947600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
26	chr3:42947200-42947600	Bivalent/Poised TSS	Osteobl	bone
27	chr3:42947200-42947800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:42947200-42948000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:42947200-42948000	Active TSS	Pancreas	Pancrea
30	chr3:42947200-42948000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr3:42947200-42948200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:42947200-42948200	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr3:42947200-42948200	Active TSS	Brain Cingulate Gyrus	brain
34	chr3:42947200-42948200	Active TSS	Fetal Brain Female	brain
35	chr3:42947200-42948200	Active TSS	Fetal Kidney	kidney
36	chr3:42947200-42948200	Active TSS	Left Ventricle	heart
37	chr3:42947200-42948200	Active TSS	Ovary	ovary
38	chr3:42947200-42948400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr3:42947200-42948400	Active TSS	Aorta	Aorta
40	chr3:42947200-42948400	Bivalent/Poised TSS	HSMM	muscle
41	chr3:42947200-42948400	Active TSS	NH-A	brain
42	chr3:42947200-42948600	Active TSS	Psoas Muscle	Psoas
43	chr3:42947200-42948800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:42947200-42948800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr3:42947400-42947600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr3:42947400-42947600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
47	chr3:42947400-42947600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr3:42947400-42947600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:42947400-42947600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:42947400-42947600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links