Variant report

Variant	rs1539248
Chromosome Location	chr10:29299339-29299340
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1248420	0.83[EUR][1000 genomes]
rs1248423	0.83[EUR][1000 genomes]
rs1248424	0.83[EUR][1000 genomes]
rs1763370	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1763383	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1773833	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1773878	0.88[ASN][1000 genomes]
rs1773879	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2484503	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484505	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783580	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2783585	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2783592	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2795100	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61838449	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs788051	0.86[EUR][1000 genomes]
rs805501	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv1046678	chr10:29242479-29378871	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv540524	chr10:29242479-29378871	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:29297400-29300000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:29297400-29300000	Weak transcription	Fetal Muscle Leg	muscle
3	chr10:29297400-29300200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:29297600-29300600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:29297800-29300000	Weak transcription	Fetal Lung	lung
6	chr10:29297800-29300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:29297800-29304400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr10:29298000-29300000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr10:29298000-29300400	Weak transcription	HepG2	liver
10	chr10:29298200-29300600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:29298600-29301000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:29298800-29300000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr10:29298800-29304600	Weak transcription	Fetal Intestine Large	intestine
14	chr10:29299000-29304400	Weak transcription	Fetal Intestine Small	intestine
15	chr10:29299200-29300200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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