Variant report

Variant	rs1870839
Chromosome Location	chr13:51473868-51473869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1328360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17589481	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296914	1.00[LWK][hapmap]
rs2441	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942941	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9526704	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526705	1.00[ASN][1000 genomes]
rs9526708	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535516	1.00[ASN][1000 genomes]
rs9535524	1.00[ASN][1000 genomes]
rs9535525	1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535528	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591369	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	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv900078	chr13:51454896-51478716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1870839	RNASEH2B	cis	Muscle Skeletal	GTEx
rs1870839	RNASEH2B-AS1	cis	Thyroid	GTEx
rs1870839	CPB2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51465600-51474600	Weak transcription	Aorta	Aorta
2	chr13:51469000-51483400	Weak transcription	Fetal Lung	lung
3	chr13:51471600-51474600	Weak transcription	Fetal Thymus	thymus
4	chr13:51471800-51474400	Enhancers	GM12878-XiMat	blood
5	chr13:51472000-51478200	Weak transcription	Thymus	Thymus
6	chr13:51472400-51474600	Weak transcription	Dnd41	blood
7	chr13:51472800-51474600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:51472800-51483400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr13:51473000-51474000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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Input of quick search could be:

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

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