Variant report

Variant	rs9822876
Chromosome Location	chr3:56594735-56594736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1045926	0.81[CHB][hapmap]
rs10865997	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10865999	0.81[CHB][hapmap]
rs11130536	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs11706624	0.81[CHB][hapmap]
rs11715395	0.81[CHB][hapmap]
rs12486047	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12631156	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13097030	0.81[CHB][hapmap]
rs1491166	0.88[CHD][hapmap]
rs17216685	0.81[JPT][hapmap]
rs2004199	0.81[CHB][hapmap];0.90[CHD][hapmap]
rs2029464	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2054987	0.81[CHB][hapmap]
rs2054988	0.81[CHB][hapmap]
rs2291499	0.81[CHB][hapmap]
rs2291501	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2317133	0.81[CHB][hapmap]
rs282524	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap]
rs282532	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs282533	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]
rs282534	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282538	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs282539	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs282543	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3732513	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4681951	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs4681963	0.81[CHB][hapmap]
rs4974218	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4974222	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6769055	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7618024	0.83[CHD][hapmap]
rs7641898	0.83[YRI][hapmap]
rs955248	0.80[AFR][1000 genomes]
rs9811046	0.81[CHB][hapmap]
rs9814014	0.81[JPT][hapmap]
rs9820759	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9823685	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs9834064	0.88[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9858728	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9862490	0.81[CHB][hapmap];0.88[CHD][hapmap];0.83[LWK][hapmap]
rs9867302	0.83[YRI][hapmap]
rs9881005	0.81[CHB][hapmap]
rs9985317	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9822876	CCDC66	cis	brain	BrainEAC
rs9822876	ERC2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56591800-56596000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:56591800-56599800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:56592400-56594800	Weak transcription	HSMM	muscle
7	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
9	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
11	chr3:56592400-56600000	Weak transcription	Ovary	ovary
12	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
14	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:56592400-56601800	Weak transcription	Lung	lung
16	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
18	chr3:56592400-56602800	Weak transcription	Gastric	stomach
19	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
20	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
21	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
22	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
24	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
25	chr3:56592600-56594800	Weak transcription	Liver	Liver
26	chr3:56592600-56594800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:56592600-56595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:56592600-56595800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:56592600-56596000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:56592600-56596000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:56592600-56598600	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:56592600-56598800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:56592600-56599600	Weak transcription	Thymus	Thymus
34	chr3:56592600-56600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:56592600-56600000	Weak transcription	Colonic Mucosa	Colon
36	chr3:56592600-56600200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:56592600-56600200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:56592600-56600200	Weak transcription	NHLF	lung
39	chr3:56592600-56601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:56592600-56601000	Weak transcription	HSMMtube	muscle
41	chr3:56592600-56601800	Weak transcription	Aorta	Aorta
42	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
44	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
45	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach
47	chr3:56592800-56594800	Weak transcription	Primary B cells from cord blood	blood
48	chr3:56592800-56594800	Weak transcription	Adipose Nuclei	Adipose
49	chr3:56592800-56594800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:56592800-56595200	Weak transcription	Muscle Satellite Cultured Cells	--

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