Variant report

Variant	rs7546886
Chromosome Location	chr1:221099995-221099996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10495156	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11118625	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11118626	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11584914	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590376	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1335914	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1414518	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17597773	0.82[MEX][hapmap]
rs1889795	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4846670	0.95[EUR][1000 genomes]
rs55703860	0.95[EUR][1000 genomes]
rs56347111	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61819203	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7546886	BPNT1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221095600-221100800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:221096600-221100200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:221096600-221100800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:221096600-221100800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:221098000-221100600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:221098000-221100600	Enhancers	NHDF-Ad	bronchial
7	chr1:221098200-221100400	Enhancers	Osteobl	bone
8	chr1:221098600-221100400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:221099000-221100200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:221099000-221100400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:221099000-221100600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:221099200-221100000	Enhancers	Fetal Muscle Leg	muscle
13	chr1:221099200-221100200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:221099200-221100200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr1:221099200-221100200	Enhancers	HSMM	muscle
16	chr1:221099200-221100600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:221099200-221102800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:221099400-221102800	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:221099600-221101200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:221099600-221101200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr1:221099600-221102800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:221099800-221104200	Weak transcription	Psoas Muscle	Psoas

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