Variant report

Variant	rs356115
Chromosome Location	chr1:55967766-55967767
allele	C/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]
rs1321119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs183065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs189593	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs356089	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356116	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs356117	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs356120	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs397876	0.81[AMR][1000 genomes]
rs418333	0.81[AMR][1000 genomes]
rs440336	0.81[AMR][1000 genomes]
rs692758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs769895	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1008241	chr1:55922008-55972596	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs356115	STAG3	trans	lymphoblastoid	seeQTL
rs356115	C1orf144	cis	Liver	GTEx
rs356115	C1orf144	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:55965800-55968200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:55966400-55974000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:55966600-55969000	Weak transcription	NHLF	lung
4	chr1:55967000-55967800	Flanking Active TSS	Thymus	Thymus
5	chr1:55967000-55967800	Enhancers	HepG2	liver
6	chr1:55967000-55969000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:55967000-55969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:55967200-55969000	Weak transcription	NHDF-Ad	bronchial
9	chr1:55967600-55968000	Enhancers	Sigmoid Colon	Sigmoid Colon

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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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