Variant report

Variant	rs56263252
Chromosome Location	chr3:56666887-56666888
allele	A/G
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	POLR2A	chr3:56666792-56667027	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:56666467-56668756	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56666598..56668908-chr3:56715764..56717337,2	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10222629	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054092	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054093	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130525	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130526	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130527	0.94[EUR][1000 genomes]
rs11712664	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11712799	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719707	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719726	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1316647	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317989	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388256	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1565378	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17216685	0.84[ASN][1000 genomes]
rs17216747	0.87[ASN][1000 genomes]
rs17288852	0.83[ASN][1000 genomes]
rs1812347	0.94[EUR][1000 genomes]
rs1873256	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291498	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291500	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317132	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282525	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282530	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282531	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282542	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3172355	1.00[ASN][1000 genomes]
rs3732505	0.95[ASN][1000 genomes]
rs4681726	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681736	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681738	0.86[ASN][1000 genomes]
rs4681903	0.95[ASN][1000 genomes]
rs4681904	0.91[ASN][1000 genomes]
rs4681937	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681955	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682001	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682002	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974221	0.83[ASN][1000 genomes]
rs4974223	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974225	0.89[EUR][1000 genomes]
rs55742226	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828519	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56028632	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56172256	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56356916	0.83[ASN][1000 genomes]
rs62251234	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62255964	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445811	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445812	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556	0.95[ASN][1000 genomes]
rs6764730	0.94[EUR][1000 genomes]
rs6767903	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794450	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799086	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7612464	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620896	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628343	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633478	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7641898	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645941	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647095	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7648297	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649872	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873840	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311609	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311612	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs953540	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809117	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809741	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9816100	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816265	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819952	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826788	0.98[ASN][1000 genomes]
rs9830377	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834239	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835134	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841851	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847362	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861577	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864701	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867302	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868059	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871265	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872059	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881152	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883842	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56263252	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs56263252	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
10	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
11	chr3:56647000-56672200	Weak transcription	Gastric	stomach
12	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
14	chr3:56647800-56668400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
17	chr3:56656200-56683000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:56657400-56683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:56657600-56675800	Strong transcription	Fetal Muscle Leg	muscle
20	chr3:56657800-56678000	Weak transcription	Fetal Brain Male	brain
21	chr3:56658400-56667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:56658400-56668200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr3:56659000-56673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:56659400-56676200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:56659600-56667600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:56659600-56668200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:56660600-56668000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:56660600-56670800	Weak transcription	Fetal Brain Female	brain
29	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:56661800-56674800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:56662200-56667000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr3:56662200-56667400	Weak transcription	NHLF	lung
33	chr3:56662200-56672800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:56662400-56667200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:56662400-56667600	Weak transcription	Brain Angular Gyrus	brain
36	chr3:56662400-56668200	Strong transcription	Fetal Stomach	stomach
37	chr3:56662400-56670800	Weak transcription	Brain Anterior Caudate	brain
38	chr3:56662400-56670800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:56662400-56672800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:56662800-56667000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr3:56663200-56667600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:56663200-56667600	Weak transcription	NHEK	skin
43	chr3:56663800-56667000	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:56663800-56667200	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:56663800-56667400	Weak transcription	Esophagus	oesophagus
46	chr3:56663800-56667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:56664000-56667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:56664000-56667000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:56664000-56667200	Weak transcription	Aorta	Aorta
50	chr3:56664000-56667200	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links