Variant report

Variant	rs873314
Chromosome Location	chr11:17462858-17462859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2074317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283257	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4148617	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs4148618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7108578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7119439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72866890	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv469895	chr11:17368270-17584220	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs873314	SAA1	cis	cerebellum	SCAN
rs873314	ABCC8	cis	Muscle Skeletal	GTEx
rs873314	DKFZp686O24166	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17454000-17464000	Weak transcription	Brain Anterior Caudate	brain
2	chr11:17454200-17465800	Weak transcription	Brain Angular Gyrus	brain
3	chr11:17456000-17469200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:17457000-17467200	Weak transcription	Fetal Brain Male	brain
5	chr11:17457200-17465400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:17457400-17464600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:17460800-17474000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:17461200-17497400	Weak transcription	Gastric	stomach
9	chr11:17462000-17465200	Strong transcription	Pancreatic Islets	Pancreatic Islet
10	chr11:17462400-17463000	ZNF genes & repeats	Dnd41	blood
11	chr11:17462400-17464800	Weak transcription	Fetal Brain Female	brain

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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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