Variant report

Variant	rs282528
Chromosome Location	chr3:56639943-56639944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10049468	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11130537	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17235670	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317134	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317244	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317252	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs282522	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282523	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282536	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs282541	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4234393	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4681734	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4681933	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681945	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681980	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4681994	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4682000	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs55831745	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55938093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56190096	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56204053	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445801	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445803	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445804	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445810	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6778373	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6781056	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6781293	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6787227	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6792321	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6802498	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6809499	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73079883	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73079884	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73079891	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73079902	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081810	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081811	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081819	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081823	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081825	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081851	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081854	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617331	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7619465	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7620259	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7631662	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7637449	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7642389	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9809309	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9833926	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835332	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839065	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9858568	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9875257	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878373	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs282528	CCDC66	cis	Thyroid	GTEx
rs282528	ARHGEF3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
2	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
3	chr3:56600600-56640000	Weak transcription	NHLF	lung
4	chr3:56603200-56650400	Weak transcription	K562	blood
5	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
7	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
8	chr3:56625200-56640000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:56625200-56640000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:56625200-56650400	Weak transcription	NHEK	skin
11	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
13	chr3:56627800-56640000	Weak transcription	GM12878-XiMat	blood
14	chr3:56628200-56640000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:56628400-56640000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:56628400-56640200	Weak transcription	Osteobl	bone
17	chr3:56628600-56640000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:56628600-56649600	Weak transcription	HepG2	liver
19	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
20	chr3:56629000-56648000	Weak transcription	NH-A	brain
21	chr3:56629600-56640000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:56629600-56640000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
24	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:56630600-56645800	Weak transcription	HSMM	muscle
26	chr3:56630800-56640000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:56630800-56645600	Weak transcription	Hela-S3	cervix
28	chr3:56631400-56641400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:56631600-56640000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:56631600-56640200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:56631600-56640200	Weak transcription	Fetal Kidney	kidney
32	chr3:56631600-56642800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:56632400-56644800	Weak transcription	A549	lung
34	chr3:56633400-56641400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:56633600-56640000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:56633600-56641400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
39	chr3:56637000-56640800	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:56637200-56640800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:56637400-56641000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:56637800-56640000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:56637800-56644200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:56638000-56640800	ZNF genes & repeats	Fetal Brain Female	brain
45	chr3:56638400-56640000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:56638400-56640800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:56638600-56640800	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr3:56638600-56641000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:56638600-56641800	Strong transcription	Primary T cells from cord blood	blood
50	chr3:56638600-56641800	Strong transcription	Brain Hippocampus Middle	brain

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