Variant report

Variant	rs11681628
Chromosome Location	chr2:190924087-190924088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10804031	0.86[CEU][hapmap]
rs13420500	0.86[CEU][hapmap]
rs3762546	0.87[CEU][hapmap]
rs3791783	0.81[EUR][1000 genomes]
rs4853626	0.86[CEU][hapmap]
rs57566211	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72909328	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72909330	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7571669	0.87[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3439178	chr2:190877215-191124499	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11681628	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs11681628	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190920200-190924600	Strong transcription	HSMM	muscle
2	chr2:190922200-190924600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:190922800-190924600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:190923600-190924800	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:190924000-190927600	Active TSS	Fetal Muscle Trunk	muscle

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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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