Variant report

Variant	rs356116
Chromosome Location	chr1:55968954-55968955
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1321119	0.83[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs183065	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs189593	0.85[EUR][1000 genomes]
rs356089	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs356091	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs356114	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs356115	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs356117	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs356120	0.85[EUR][1000 genomes]
rs692758	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs769895	0.91[AMR][1000 genomes];0.85[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs356116	PTPN13	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:55966400-55974000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:55966600-55969000	Weak transcription	NHLF	lung
3	chr1:55967000-55969000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:55967000-55969000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:55967200-55969000	Weak transcription	NHDF-Ad	bronchial
6	chr1:55967800-55969400	Weak transcription	HepG2	liver
7	chr1:55968000-55969000	Weak transcription	Fetal Stomach	stomach
8	chr1:55968000-55969000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:55968000-55969000	Weak transcription	Small Intestine	intestine
10	chr1:55968400-55969600	Weak transcription	Thymus	Thymus
11	chr1:55968600-55970400	Weak transcription	Right Atrium	heart
12	chr1:55968600-55971400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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