Variant report

Variant	rs13180690
Chromosome Location	chr5:58789176-58789177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10514861	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs10514862	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs167161	1.00[CHB][hapmap]
rs16889907	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs16889919	1.00[JPT][hapmap]
rs16889921	0.81[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs17796734	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[ASN][1000 genomes]
rs28725359	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58922738	1.00[ASN][1000 genomes]
rs6885378	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6896121	1.00[ASN][1000 genomes]
rs7706227	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7707043	0.80[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13180690	GAPT	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58784000-58791600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr5:58784000-58792200	Weak transcription	Psoas Muscle	Psoas
3	chr5:58784000-58793200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:58784600-58791000	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:58784600-58797000	Weak transcription	Fetal Lung	lung
6	chr5:58784800-58790000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:58787000-58803800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:58787200-58789200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:58788400-58789200	Weak transcription	A549	lung

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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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