Variant report

Variant	rs12631156
Chromosome Location	chr3:56625610-56625611
allele	A/G
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	CEBPB	chr3:56625349-56625694	IMR90	lung:	n/a	n/a
2	POLR2A	chr3:56622643-56625622	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCDC66	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10865997	0.84[AMR][1000 genomes]
rs12486047	0.84[AMR][1000 genomes]
rs17216685	0.81[AMR][1000 genomes]
rs282524	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs282526	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs282532	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs282533	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282534	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282537	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282538	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282539	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282543	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732513	0.84[ASN][1000 genomes]
rs4974218	0.84[AMR][1000 genomes]
rs4974222	0.84[AMR][1000 genomes]
rs66873962	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6769055	0.84[AMR][1000 genomes]
rs7640995	0.84[ASN][1000 genomes]
rs9822876	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9823685	0.81[AMR][1000 genomes]
rs9834064	0.81[AMR][1000 genomes]
rs9985317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv528087	chr3:56608033-56628031	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12631156	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
2	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
3	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
4	chr3:56600600-56640000	Weak transcription	NHLF	lung
5	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
6	chr3:56603200-56650400	Weak transcription	K562	blood
7	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:56604200-56627600	Weak transcription	Brain Angular Gyrus	brain
9	chr3:56604600-56625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel
11	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
12	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
13	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
14	chr3:56606000-56627600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:56606000-56627600	Weak transcription	Left Ventricle	heart
16	chr3:56606000-56629200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
18	chr3:56606600-56627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:56606800-56627600	Weak transcription	Osteobl	bone
20	chr3:56607600-56627200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:56607800-56627400	Weak transcription	Brain Anterior Caudate	brain
22	chr3:56607800-56627600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:56607800-56627600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:56607800-56627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:56607800-56627600	Weak transcription	NHDF-Ad	bronchial
26	chr3:56607800-56627800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:56607800-56629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
29	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
30	chr3:56608200-56627600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:56609000-56626800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:56610000-56627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:56610000-56627600	Weak transcription	HSMM	muscle
35	chr3:56616200-56633800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:56616400-56639400	Weak transcription	Lung	lung
37	chr3:56616600-56627000	Weak transcription	Liver	Liver
38	chr3:56617200-56626400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:56617200-56626400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:56617200-56626800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:56617200-56627000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:56617200-56627000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:56617200-56627000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:56617200-56627200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:56617200-56627400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:56617200-56627600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:56617200-56627600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:56617200-56629000	Weak transcription	Fetal Brain Female	brain
49	chr3:56617200-56629400	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:56617200-56629400	Weak transcription	Rectal Mucosa Donor 29	rectum

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