Variant report

Variant	rs9871265
Chromosome Location	chr3:56684765-56684766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56679500..56681648-chr3:56682849..56685155,2	MCF-7	breast:
2	chr3:56679657..56682085-chr3:56683024..56685960,3	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10222629	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054092	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054093	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130525	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130526	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130527	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11130542	0.83[EUR][1000 genomes]
rs11712664	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11712799	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719726	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075010	0.83[CHB][hapmap]
rs1316647	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388256	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1565378	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17216657	0.83[CHB][hapmap]
rs17216685	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17216747	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs17288852	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs1812347	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1873256	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317132	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282531	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282542	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3172355	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3732505	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4681726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681736	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681738	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681739	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4681903	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4681904	0.91[ASN][1000 genomes]
rs4681937	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681955	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682002	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682008	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4974221	0.83[ASN][1000 genomes]
rs4974223	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974225	0.85[EUR][1000 genomes]
rs55742226	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828519	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56028632	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56172256	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56263252	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56356916	0.83[ASN][1000 genomes]
rs62251234	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62255964	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6445811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs6764730	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6767903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6799086	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72624856	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7612464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620896	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628343	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633478	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639731	0.82[AMR][1000 genomes]
rs7640995	0.82[AMR][1000 genomes]
rs7641898	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645941	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647095	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7648297	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649872	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873840	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311612	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs953540	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809117	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809741	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9814014	0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs9816100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819952	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826788	0.98[ASN][1000 genomes]
rs9830377	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834239	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835134	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841851	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867302	0.86[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868059	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881152	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883842	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9871265	CCDC66	cis	Whole Blood	GTEx
rs9871265	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
8	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
10	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:56664000-56688000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:56664000-56694800	Weak transcription	Stomach Mucosa	stomach
13	chr3:56664800-56687400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:56664800-56711000	Strong transcription	Dnd41	blood
15	chr3:56665000-56687800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:56665000-56690400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:56665000-56707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:56665200-56686600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:56665200-56691800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:56665200-56698800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr3:56665200-56707200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:56665400-56687000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:56665800-56687400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:56665800-56687400	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:56666000-56686800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:56666200-56708000	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:56668000-56688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:56668000-56707200	Strong transcription	Placenta	Placenta
29	chr3:56669200-56686400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:56669600-56703800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:56670000-56687000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:56670600-56687000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:56670800-56687000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:56672600-56686600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:56673600-56687600	Strong transcription	GM12878-XiMat	blood
36	chr3:56675600-56686000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr3:56675600-56702200	Weak transcription	K562	blood
38	chr3:56675800-56685400	Weak transcription	Lung	lung
39	chr3:56675800-56686000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:56675800-56686200	Weak transcription	Spleen	Spleen
41	chr3:56675800-56687600	Weak transcription	Brain Anterior Caudate	brain
42	chr3:56675800-56687600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:56675800-56688600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:56675800-56688800	Weak transcription	Aorta	Aorta
45	chr3:56675800-56691600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:56675800-56691600	Weak transcription	HSMMtube	muscle
47	chr3:56675800-56691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:56675800-56692400	Weak transcription	Right Ventricle	heart
49	chr3:56675800-56693400	Weak transcription	Colonic Mucosa	Colon
50	chr3:56675800-56695200	Weak transcription	Gastric	stomach

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