Variant report

Variant	rs953540
Chromosome Location	chr3:56691788-56691789
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56690378..56691903-chr3:56713310..56716081,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10222629	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054092	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054093	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865997	0.87[YRI][hapmap]
rs11130525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130527	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs11130542	0.83[EUR][1000 genomes]
rs11712664	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[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719726	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486047	0.87[YRI][hapmap]
rs13075010	0.83[CHB][hapmap]
rs1316647	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317989	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1565378	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17216657	0.83[CHB][hapmap]
rs17216685	0.95[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	0.89[EUR][1000 genomes]
rs1873256	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291500	1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs282524	0.87[YRI][hapmap]
rs282525	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282531	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282533	0.81[YRI][hapmap]
rs282542	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3172355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3732505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4681726	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681736	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4681738	0.81[AFR][1000 genomes];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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4681904	0.91[ASN][1000 genomes]
rs4681937	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682001	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682002	0.89[AFR][1000 genomes];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[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4974225	0.85[EUR][1000 genomes]
rs55742226	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55828519	0.93[AFR][1000 genomes];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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6764730	0.89[EUR][1000 genomes]
rs6767903	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6769055	0.87[YRI][hapmap]
rs6794450	0.95[CHB][hapmap];1.00[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[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620896	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7628343	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633478	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639731	0.82[AMR][1000 genomes]
rs7640995	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7641898	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7645941	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647095	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7648297	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649872	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873840	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9311609	1.00[CHB][hapmap];1.00[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]
rs9311612	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809117	0.97[AFR][1000 genomes];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	0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs9816100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816265	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826788	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9830377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834064	0.87[YRI][hapmap]
rs9834239	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835134	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9841851	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847362	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9861577	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864701	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867302	1.00[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]
rs9868059	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871265	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872059	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881152	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs953540	CCDC66	cis	multi-tissue	Pritchard
rs953540	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs953540	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	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
7	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
9	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:56664000-56694800	Weak transcription	Stomach Mucosa	stomach
11	chr3:56664800-56711000	Strong transcription	Dnd41	blood
12	chr3:56665000-56707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:56665200-56691800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:56665200-56698800	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:56665200-56707200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:56666200-56708000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr3:56668000-56707200	Strong transcription	Placenta	Placenta
18	chr3:56669600-56703800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:56675600-56702200	Weak transcription	K562	blood
20	chr3:56675800-56691800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:56675800-56692400	Weak transcription	Right Ventricle	heart
22	chr3:56675800-56693400	Weak transcription	Colonic Mucosa	Colon
23	chr3:56675800-56695200	Weak transcription	Gastric	stomach
24	chr3:56675800-56707000	Weak transcription	Esophagus	oesophagus
25	chr3:56675800-56716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:56676000-56705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:56677000-56696600	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:56677200-56705400	Strong transcription	Primary T cells from cord blood	blood
29	chr3:56680400-56692600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:56682400-56694000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:56683600-56702200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:56684000-56693200	Weak transcription	Fetal Brain Male	brain
33	chr3:56684000-56705400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:56684200-56691800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:56684400-56696000	Strong transcription	Fetal Muscle Leg	muscle
36	chr3:56684400-56698200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:56684400-56715200	Weak transcription	Fetal Heart	heart
38	chr3:56684800-56691800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:56684800-56695800	Strong transcription	Fetal Lung	lung
40	chr3:56684800-56706200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:56684800-56707800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:56685000-56707200	Strong transcription	Osteobl	bone
43	chr3:56685400-56700000	Strong transcription	Fetal Stomach	stomach
44	chr3:56685400-56707400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:56685800-56693200	Weak transcription	Pancreas	Pancrea
46	chr3:56686600-56691800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:56686600-56693000	Weak transcription	Fetal Kidney	kidney
48	chr3:56687000-56691800	Weak transcription	HepG2	liver
49	chr3:56687000-56705400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:56687200-56691800	Weak transcription	Lung	lung

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