Variant report

Variant	rs955248
Chromosome Location	chr3:56616813-56616814
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10865997	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12486047	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12496217	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282524	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs282526	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs282537	1.00[EUR][1000 genomes]
rs35349208	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs3732513	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4974218	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4974222	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs55810735	0.86[EUR][1000 genomes]
rs66873962	0.91[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6769055	0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs6799711	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7639731	0.87[EUR][1000 genomes]
rs7640995	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9822876	0.80[AFR][1000 genomes]
rs9823685	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9834064	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9873754	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv822097	chr3:56607112-56620842	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv435762	chr3:56607518-56622066	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv19690	chr3:56607723-56621531	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv822099	chr3:56607804-56620842	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1827962	chr3:56607811-56617333	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1830828	chr3:56607811-56617333	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1832534	chr3:56607811-56617333	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1831026	chr3:56607811-56620106	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1832365	chr3:56607811-56620106	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1826366	chr3:56607826-56620842	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1830577	chr3:56607826-56620842	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv963260	chr3:56608026-56620152	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1825630	chr3:56608033-56620106	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1827186	chr3:56608033-56620106	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1827416	chr3:56608033-56620106	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	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
rs955248	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr3:56604600-56624600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:56604600-56625000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:56604600-56625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel
13	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
14	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
15	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
16	chr3:56606000-56617000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:56606000-56627600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:56606000-56627600	Weak transcription	Left Ventricle	heart
19	chr3:56606000-56629200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
21	chr3:56606600-56617000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr3:56606600-56627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:56606800-56624000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:56606800-56627600	Weak transcription	Osteobl	bone
25	chr3:56607000-56624200	Weak transcription	HepG2	liver
26	chr3:56607000-56624400	Weak transcription	NH-A	brain
27	chr3:56607600-56627200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:56607800-56617000	Weak transcription	Fetal Brain Female	brain
29	chr3:56607800-56617000	Weak transcription	Fetal Lung	lung
30	chr3:56607800-56617000	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:56607800-56624000	Weak transcription	HMEC	breast
32	chr3:56607800-56624200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:56607800-56627400	Weak transcription	Brain Anterior Caudate	brain
34	chr3:56607800-56627600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:56607800-56627600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:56607800-56627600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:56607800-56627600	Weak transcription	NHDF-Ad	bronchial
38	chr3:56607800-56627800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:56607800-56629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:56607800-56639800	Weak transcription	HSMMtube	muscle
41	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
42	chr3:56608200-56617800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:56608200-56627600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr3:56608600-56624000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:56609000-56626800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:56609400-56624000	Weak transcription	Ovary	ovary
47	chr3:56609400-56638600	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:56609600-56624400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:56610000-56627600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:56610000-56627600	Weak transcription	HSMM	muscle

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