Variant report

Variant	rs3846063
Chromosome Location	chr3:42803828-42803829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42798882..42800996-chr3:42802140..42804185,2	K562	blood:
2	chr3:42791485..42794252-chr3:42803648..42805435,2	K562	blood:
3	chr3:42792752..42794704-chr3:42802207..42805435,3	K562	blood:
4	chr3:42796140..42798050-chr3:42801368..42804341,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10490794	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10865922	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs11129975	0.90[EUR][1000 genomes]
rs11129976	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11129977	0.89[EUR][1000 genomes]
rs11718476	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11922251	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11922832	0.96[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs11929390	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12491179	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12635736	0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs12639142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13070029	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13070345	0.87[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap]
rs13096498	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2240859	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2372110	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339671	0.96[EUR][1000 genomes]
rs339684	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs339731	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34868846	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35584330	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3843369	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3895740	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3907218	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs3912104	0.87[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs4683332	0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs4683335	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6442067	0.95[EUR][1000 genomes]
rs6779561	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7639170	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7639483	0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs7641046	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs9830553	0.86[CHB][hapmap];0.85[JPT][hapmap]

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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3846063	CCDC13	cis	parietal	SCAN
rs3846063	CCDC13	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42778000-42811000	Weak transcription	Spleen	Spleen
2	chr3:42788600-42804200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:42789800-42807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:42791000-42804000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:42791800-42804000	Weak transcription	Right Ventricle	heart
6	chr3:42791800-42807200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:42793600-42811000	Weak transcription	Lung	lung
8	chr3:42795600-42814000	Weak transcription	Gastric	stomach
9	chr3:42795600-42814400	Weak transcription	Aorta	Aorta
10	chr3:42798600-42804000	Weak transcription	Stomach Mucosa	stomach
11	chr3:42800400-42808600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:42802200-42805000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:42802400-42804600	Enhancers	Liver	Liver
14	chr3:42802400-42804600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:42802400-42804800	Enhancers	Adipose Nuclei	Adipose
16	chr3:42802400-42804800	Enhancers	NHDF-Ad	bronchial
17	chr3:42802400-42805000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:42802400-42805000	Enhancers	HepG2	liver
19	chr3:42802400-42806400	Enhancers	Placenta	Placenta
20	chr3:42802600-42804000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:42802600-42804200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:42802600-42804600	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:42802600-42804600	Enhancers	Brain Hippocampus Middle	brain
24	chr3:42802600-42805000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr3:42802600-42805000	Enhancers	Brain Anterior Caudate	brain
26	chr3:42802600-42805000	Enhancers	Osteobl	bone
27	chr3:42802600-42805400	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:42802600-42806200	Enhancers	Brain Substantia Nigra	brain
29	chr3:42802800-42804400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:42802800-42804400	Weak transcription	A549	lung
31	chr3:42802800-42804600	Enhancers	Primary B cells from cord blood	blood
32	chr3:42802800-42804600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:42803000-42804400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:42803000-42804600	Enhancers	NHLF	lung
35	chr3:42803000-42814200	Weak transcription	Right Atrium	heart
36	chr3:42803200-42804200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:42803200-42804400	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:42803200-42806000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:42803400-42804200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr3:42803400-42804200	Weak transcription	Esophagus	oesophagus
41	chr3:42803400-42804800	Enhancers	Fetal Intestine Small	intestine
42	chr3:42803400-42805000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:42803400-42805800	Weak transcription	Colonic Mucosa	Colon
44	chr3:42803400-42806000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:42803400-42806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:42803600-42805000	Enhancers	Stomach Smooth Muscle	stomach
47	chr3:42803800-42804200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:42803800-42804400	Enhancers	Fetal Thymus	thymus
49	chr3:42803800-42804400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:42803800-42804600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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