Variant report

Variant	rs2840827
Chromosome Location	chr6:133022239-133022240
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17604042	0.82[YRI][hapmap]
rs2179536	0.82[YRI][hapmap]
rs2294757	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2745434	0.82[YRI][hapmap]
rs3798793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897607	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897612	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs6915807	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6938367	0.82[YRI][hapmap]
rs742516	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.81[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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2840827	AHI1	cis	cerebellum	SCAN
rs2840827	MAP3K5	cis	cerebellum	SCAN
rs2840827	VNN1	cis	lung	GTEx
rs2840827	PDE7B	cis	parietal	SCAN
rs2840827	VNN1	cis	multi-tissue	Pritchard
rs2840827	VNN1	cis	Whole Blood	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133017800-133032200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:133018200-133028400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr6:133020000-133024000	Weak transcription	Aorta	Aorta
4	chr6:133020400-133023000	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:133020400-133023600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr6:133021200-133022600	Weak transcription	Liver	Liver

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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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