Variant report

Variant	rs339705
Chromosome Location	chr3:42724448-42724449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42694748..42699561-chr3:42722251..42726025,6	K562	blood:
2	chr3:42709626..42711413-chr3:42723979..42726333,2	MCF-7	breast:
3	chr3:42720527..42722728-chr3:42723710..42726104,2	MCF-7	breast:
4	chr3:42709094..42711922-chr3:42723426..42725135,3	K562	blood:
5	chr3:42717924..42720183-chr3:42723570..42725639,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC13-1	chr3:42724307-42724788	XLOC_003100

Variant related genes	Relation type
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000240203	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs13067987	0.90[EUR][1000 genomes]
rs13085143	0.88[CEU][hapmap]
rs13086680	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13100261	0.89[CEU][hapmap]
rs17030458	0.89[EUR][1000 genomes]
rs2290976	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs339708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35216140	0.89[EUR][1000 genomes]
rs35871059	0.89[EUR][1000 genomes]
rs36043081	0.89[EUR][1000 genomes]
rs3733059	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3733061	0.86[AMR][1000 genomes]
rs3900780	0.90[EUR][1000 genomes]
rs55994846	0.85[EUR][1000 genomes]
rs56047094	0.89[EUR][1000 genomes]
rs58825152	0.84[EUR][1000 genomes]
rs60535002	0.89[EUR][1000 genomes]
rs66933062	0.82[EUR][1000 genomes]
rs67583158	0.89[EUR][1000 genomes]
rs6771105	0.89[EUR][1000 genomes]
rs67832425	0.89[EUR][1000 genomes]
rs6790204	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs6797491	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs6797545	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs68004576	0.89[EUR][1000 genomes]
rs71323162	0.82[EUR][1000 genomes]
rs72864022	0.80[EUR][1000 genomes]
rs73829255	0.89[EUR][1000 genomes]
rs7614219	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs7616701	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7623867	0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs339705	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42718000-42724800	Weak transcription	Right Atrium	heart
2	chr3:42720200-42725000	Weak transcription	Right Ventricle	heart
3	chr3:42722400-42725000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:42722400-42725000	Weak transcription	NH-A	brain
5	chr3:42722400-42725800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:42722600-42724600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:42722600-42724800	Weak transcription	HSMM	muscle
8	chr3:42722600-42725000	Weak transcription	NHLF	lung
9	chr3:42722800-42724800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:42722800-42724800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:42722800-42724800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:42722800-42724800	Weak transcription	NHDF-Ad	bronchial
13	chr3:42724000-42726400	Enhancers	Placenta	Placenta
14	chr3:42724200-42724600	Enhancers	Psoas Muscle	Psoas
15	chr3:42724200-42725200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:42724200-42725400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr3:42724200-42726200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:42724200-42726200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:42724200-42726200	Enhancers	Fetal Muscle Leg	muscle
20	chr3:42724200-42727000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:42724200-42727000	Enhancers	HSMMtube	muscle
22	chr3:42724200-42727400	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:42724200-42727400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:42724200-42729400	Enhancers	Fetal Heart	heart
25	chr3:42724400-42725000	Weak transcription	Left Ventricle	heart
26	chr3:42724400-42725200	Bivalent Enhancer	HepG2	liver
27	chr3:42724400-42726400	Enhancers	Aorta	Aorta
28	chr3:42724400-42726600	Enhancers	Brain Anterior Caudate	brain
29	chr3:42724400-42726800	Enhancers	Brain Angular Gyrus	brain

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