Variant report

Variant	rs1039296
Chromosome Location	chr1:56103659-56103660
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1165472	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1392140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1499659	0.88[JPT][hapmap]
rs1533318	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6659204	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6700588	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769995	0.91[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	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv526148	chr1:56101597-56146450	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1039296	BSND	cis	cerebellum	SCAN
rs1039296	DAB1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56089000-56104000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:56098800-56105800	Weak transcription	Fetal Stomach	stomach
3	chr1:56099000-56105200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:56099000-56106600	Weak transcription	Ovary	ovary
5	chr1:56099200-56105800	Weak transcription	Fetal Kidney	kidney
6	chr1:56100600-56106600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:56100800-56104800	Weak transcription	Hela-S3	cervix
8	chr1:56100800-56106600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:56101200-56104200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:56101200-56105000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:56101200-56105800	Weak transcription	Psoas Muscle	Psoas
12	chr1:56101800-56106600	Weak transcription	Fetal Lung	lung
13	chr1:56102200-56106000	Weak transcription	NHLF	lung
14	chr1:56102400-56105200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:56102400-56106000	Weak transcription	Aorta	Aorta
16	chr1:56102400-56106400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:56102600-56105800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:56102800-56105000	Weak transcription	Osteobl	bone
19	chr1:56103000-56106400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:56103400-56106000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:56103400-56106400	Weak transcription	NHDF-Ad	bronchial
22	chr1:56103400-56107000	Weak transcription	Gastric	stomach

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