Variant report

Variant	rs3732505
Chromosome Location	chr3:56652058-56652059
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10222629	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1054092	0.91[ASN][1000 genomes]
rs1054093	0.91[ASN][1000 genomes]
rs10865997	0.81[MEX][hapmap]
rs11130525	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11130526	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11130527	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11712664	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11712799	0.84[ASN][1000 genomes]
rs11719707	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[ASN][1000 genomes]
rs11719726	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12486047	0.81[MEX][hapmap]
rs13075010	0.83[CHB][hapmap]
rs1316647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13317989	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs1388256	0.81[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1565378	0.89[ASN][1000 genomes]
rs17216657	0.82[CHB][hapmap]
rs17216685	0.94[ASW][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17216747	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs17288852	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs1873256	0.90[ASN][1000 genomes]
rs2291498	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2291500	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2317132	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs282524	0.81[MEX][hapmap]
rs282525	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs282530	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs282531	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs282542	0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3172355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681726	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs4681736	0.88[ASN][1000 genomes]
rs4681738	0.82[ASN][1000 genomes]
rs4681903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681904	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681937	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4681955	0.95[ASN][1000 genomes]
rs4682001	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[ASN][1000 genomes]
rs4682002	0.88[ASN][1000 genomes]
rs4974221	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4974223	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55742226	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55828519	0.90[ASN][1000 genomes]
rs55865922	0.81[ASN][1000 genomes]
rs56126040	0.81[ASN][1000 genomes]
rs56172256	0.82[ASN][1000 genomes]
rs56263252	0.95[ASN][1000 genomes]
rs56356916	0.87[ASN][1000 genomes]
rs62251234	0.91[ASN][1000 genomes]
rs62255964	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6445811	0.95[ASN][1000 genomes]
rs6445812	0.95[ASN][1000 genomes]
rs6556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767903	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6769055	0.81[MEX][hapmap]
rs6794450	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6799086	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7612464	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs7620896	0.88[ASN][1000 genomes]
rs7628343	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7633478	0.94[ASN][1000 genomes]
rs7641898	0.91[ASN][1000 genomes]
rs7645941	0.91[ASN][1000 genomes]
rs7647095	0.91[ASN][1000 genomes]
rs7648297	0.91[ASN][1000 genomes]
rs7649872	0.95[ASN][1000 genomes]
rs873840	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs9311609	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs9311612	0.91[ASN][1000 genomes]
rs953540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9809117	0.94[ASN][1000 genomes]
rs9814014	0.95[JPT][hapmap]
rs9816100	0.95[ASN][1000 genomes]
rs9816265	0.95[ASN][1000 genomes]
rs9819952	0.95[ASN][1000 genomes]
rs9826788	0.94[ASN][1000 genomes]
rs9830377	0.93[ASN][1000 genomes]
rs9834064	0.81[MEX][hapmap]
rs9834239	0.93[ASN][1000 genomes]
rs9835134	0.91[ASN][1000 genomes]
rs9841851	0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9847362	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs9861577	0.91[ASN][1000 genomes]
rs9864701	0.95[ASN][1000 genomes]
rs9867302	0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[ASN][1000 genomes]
rs9868059	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9871265	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9872059	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs9881152	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9883842	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3732505	CCDC66	cis	lymphoblastoid	seeQTL
rs3732505	FLNB	cis	cerebellum	SCAN
rs3732505	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs3732505	CCDC66	cis	Whole Blood	GTEx
rs3732505	LOC285331	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
3	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
15	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr3:56645600-56653400	Weak transcription	Fetal Heart	heart
22	chr3:56645600-56656000	Strong transcription	Fetal Intestine Large	intestine
23	chr3:56645600-56656000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:56645600-56664800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:56645600-56665800	Strong transcription	Hela-S3	cervix
26	chr3:56645800-56662000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:56645800-56663800	Strong transcription	HSMM	muscle
28	chr3:56646000-56662800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:56646200-56659200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
31	chr3:56646800-56658800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:56646800-56659200	Weak transcription	Fetal Intestine Small	intestine
33	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
34	chr3:56647000-56658400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:56647000-56662000	Weak transcription	Esophagus	oesophagus
36	chr3:56647000-56663000	Strong transcription	Liver	Liver
37	chr3:56647000-56664000	Strong transcription	Adipose Nuclei	Adipose
38	chr3:56647000-56666800	Weak transcription	Lung	lung
39	chr3:56647000-56672200	Weak transcription	Gastric	stomach
40	chr3:56647200-56662600	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:56647200-56664000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:56647200-56664000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:56647400-56655400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:56647400-56663800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:56647400-56664000	Strong transcription	Primary T cells from cord blood	blood
46	chr3:56647400-56664200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:56647400-56664400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
50	chr3:56647600-56655400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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