Variant report

Variant	rs1539058
Chromosome Location	chr1:56753249-56753250
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12118755	0.84[EUR][1000 genomes]
rs12140921	0.81[EUR][1000 genomes]
rs1341339	0.86[CEU][hapmap]
rs1341345	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1341352	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1417771	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs1539059	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17423986	0.80[EUR][1000 genomes]
rs2793678	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793685	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793686	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2793687	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6673309	0.86[CEU][hapmap];0.81[TSI][hapmap]
rs947251	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][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	nsv1006422	chr1:56734772-56828606	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv534972	chr1:56734772-56828606	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1539058	C8B	cis	parietal	SCAN
rs1539058	DMRTB1	cis	cerebellum	SCAN
rs1539058	FGGY	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56745400-56757000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:56748400-56759600	Weak transcription	Aorta	Aorta
3	chr1:56750000-56753400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:56751000-56753600	Enhancers	Placenta	Placenta
5	chr1:56751000-56753600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:56751200-56753400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:56751200-56753400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr1:56751200-56756000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:56751400-56756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:56751400-56757600	Weak transcription	Pancreas	Pancrea
11	chr1:56751800-56756800	Weak transcription	Lung	lung
12	chr1:56752000-56756800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:56752000-56757000	Weak transcription	Fetal Stomach	stomach
14	chr1:56752000-56757000	Weak transcription	HSMMtube	muscle
15	chr1:56752200-56753600	Weak transcription	HepG2	liver
16	chr1:56752600-56756800	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:56752800-56755000	Weak transcription	Left Ventricle	heart
18	chr1:56752800-56756800	Weak transcription	Adipose Nuclei	Adipose
19	chr1:56752800-56756800	Weak transcription	Psoas Muscle	Psoas
20	chr1:56752800-56756800	Weak transcription	Right Atrium	heart
21	chr1:56752800-56756800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:56753000-56753400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:56753000-56754200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:56753200-56753600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:56753200-56754000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:56753200-56756800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:56753200-56763600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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