Variant report

Variant	rs282533
Chromosome Location	chr3:56645448-56645449
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1045926	0.83[CHB][hapmap]
rs10865997	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10865999	0.83[CHB][hapmap]
rs11130536	0.82[CHB][hapmap]
rs11130538	0.81[CHB][hapmap]
rs11706624	0.83[CHB][hapmap]
rs11715395	0.83[CHB][hapmap]
rs12486047	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes]
rs12631156	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13097030	0.83[CHB][hapmap]
rs1316647	0.81[YRI][hapmap]
rs17056878	0.82[CHB][hapmap]
rs2004199	0.82[CHB][hapmap]
rs2029464	0.82[CHB][hapmap]
rs2054987	0.83[CHB][hapmap]
rs2054988	0.83[CHB][hapmap]
rs2291499	0.83[CHB][hapmap]
rs2291501	0.82[CHB][hapmap]
rs2317133	0.83[CHB][hapmap]
rs282524	0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282526	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282532	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282534	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282537	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs282538	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282539	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282543	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732513	0.83[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4681951	0.82[CHB][hapmap]
rs4681963	0.83[CHB][hapmap]
rs4974218	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4974222	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs66873962	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6769055	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7612599	0.81[CHB][hapmap]
rs7639731	0.81[ASN][1000 genomes]
rs7640995	0.85[ASN][1000 genomes]
rs7641898	0.85[YRI][hapmap]
rs873840	0.80[YRI][hapmap]
rs953540	0.81[YRI][hapmap]
rs9811046	0.83[CHB][hapmap]
rs9820759	0.82[CHB][hapmap]
rs9822876	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9823685	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs9834064	0.83[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs9858728	0.82[CHB][hapmap]
rs9862490	0.82[CHB][hapmap]
rs9867302	0.83[YRI][hapmap]
rs9881005	0.83[CHB][hapmap]
rs9985317	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs282533	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	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56629000-56647400	Weak transcription	HUVEC	blood vessel
9	chr3:56629000-56648000	Weak transcription	NH-A	brain
10	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
11	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:56630600-56645800	Weak transcription	HSMM	muscle
13	chr3:56630800-56645600	Weak transcription	Hela-S3	cervix
14	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
16	chr3:56640000-56650000	Weak transcription	HMEC	breast
17	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:56640600-56646800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:56640600-56647200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:56640600-56647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
22	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:56640800-56645600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:56640800-56645600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:56640800-56645600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:56640800-56645600	Weak transcription	Fetal Intestine Large	intestine
28	chr3:56640800-56645600	Weak transcription	Placenta	Placenta
29	chr3:56640800-56645800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:56640800-56646000	Weak transcription	Spleen	Spleen
31	chr3:56640800-56646200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:56640800-56646400	Weak transcription	Esophagus	oesophagus
33	chr3:56640800-56646400	Weak transcription	Gastric	stomach
34	chr3:56640800-56646600	Weak transcription	Aorta	Aorta
35	chr3:56640800-56646800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:56640800-56647000	Weak transcription	Liver	Liver
37	chr3:56640800-56647200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr3:56640800-56647400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:56640800-56647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:56640800-56647400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:56640800-56647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:56640800-56647600	Weak transcription	Brain Angular Gyrus	brain
43	chr3:56640800-56647800	Weak transcription	Dnd41	blood
44	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:56640800-56649400	Weak transcription	Osteobl	bone
46	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
47	chr3:56640800-56650400	Weak transcription	NHLF	lung
48	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
49	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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