Variant report

Variant	rs11712664
Chromosome Location	chr3:56664048-56664049
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	POLR2A	chr3:56662753-56664078	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
FAM208A	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10222629	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1054092	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1054093	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11130525	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130526	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130527	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11712799	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719707	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719726	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316647	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317989	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1388256	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1565378	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17216747	0.81[ASN][1000 genomes]
rs1812347	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1873256	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291498	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291500	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2317132	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282525	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282530	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282531	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282542	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3172355	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3732505	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4681726	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681736	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681738	0.80[ASN][1000 genomes]
rs4681903	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4681904	0.86[ASN][1000 genomes]
rs4681937	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681955	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682001	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682002	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4974223	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974225	0.88[EUR][1000 genomes]
rs55742226	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55828519	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56172256	0.80[ASN][1000 genomes]
rs56263252	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62251234	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62255964	0.85[EUR][1000 genomes]
rs6445811	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445812	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6764730	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6767903	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794450	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6799086	0.84[EUR][1000 genomes]
rs7612464	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620896	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628343	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7633478	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641898	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7645941	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647095	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648297	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649872	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873840	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9311609	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9311612	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953540	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809117	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9809741	0.80[EUR][1000 genomes]
rs9816100	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9816265	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9819952	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9826788	0.93[ASN][1000 genomes]
rs9830377	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9834239	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9835134	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9841851	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847362	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861577	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864701	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9867302	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868059	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9871265	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872059	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9881152	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9883842	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712664	CCDC66	cis	Whole Blood	GTEx
rs11712664	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
13	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
14	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
15	chr3:56647000-56666800	Weak transcription	Lung	lung
16	chr3:56647000-56672200	Weak transcription	Gastric	stomach
17	chr3:56647400-56664200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:56647400-56664400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
21	chr3:56647600-56664200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:56647800-56668400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:56649800-56664200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
26	chr3:56654000-56666200	Weak transcription	Ovary	ovary
27	chr3:56654600-56666800	Weak transcription	Colonic Mucosa	Colon
28	chr3:56654600-56666800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:56655000-56666200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:56656200-56683000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:56657400-56683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:56657600-56675800	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:56657800-56678000	Weak transcription	Fetal Brain Male	brain
34	chr3:56658000-56666800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:56658400-56667400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:56658400-56668200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr3:56659000-56666600	Weak transcription	Fetal Heart	heart
38	chr3:56659000-56666800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr3:56659000-56673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:56659200-56666600	Weak transcription	Brain Substantia Nigra	brain
41	chr3:56659200-56666800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:56659400-56666000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:56659400-56676200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:56659600-56666000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:56659600-56666800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:56659600-56667600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:56659600-56668200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:56660000-56666800	Weak transcription	Spleen	Spleen
49	chr3:56660600-56668000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:56660600-56670800	Weak transcription	Fetal Brain Female	brain

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