Variant report

Variant	rs1357783
Chromosome Location	chr1:57942814-57942815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10889047	0.87[EUR][1000 genomes]
rs1155680	0.83[EUR][1000 genomes]
rs12044871	0.96[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs12044874	0.86[EUR][1000 genomes]
rs12044912	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12046102	0.81[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs12132685	0.81[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs12752978	0.85[EUR][1000 genomes]
rs1334239	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1334240	0.83[EUR][1000 genomes]
rs17459948	0.93[CEU][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2781325	0.89[EUR][1000 genomes]
rs4279875	0.93[MEX][hapmap];0.84[TSI][hapmap]
rs9436130	0.89[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1357783	C8A	cis	cerebellum	SCAN
rs1357783	TMEM59	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57940200-57949600	Weak transcription	NHDF-Ad	bronchial
2	chr1:57940800-57954800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:57942400-57943000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:57942400-57943000	Enhancers	Small Intestine	intestine
5	chr1:57942600-57943000	Weak transcription	Stomach Mucosa	stomach

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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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