Variant report

Variant	rs161287
Chromosome Location	chr7:78260373-78260374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs106051	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs161286	0.87[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs161288	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs191181	0.86[AFR][1000 genomes]
rs319861	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs319862	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs38098	0.85[CEU][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs38100	0.91[JPT][hapmap]
rs38103	0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs38104	0.95[JPT][hapmap];0.84[MEX][hapmap]
rs38107	0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs38109	0.86[CEU][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs38114	0.86[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs38120	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs161287	MDH2	cis	cerebellum	SCAN
rs161287	SNORA14A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78252600-78266400	Weak transcription	Aorta	Aorta
2	chr7:78254200-78268800	Weak transcription	Brain Germinal Matrix	brain
3	chr7:78257000-78264600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:78257600-78263600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr7:78257600-78266200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr7:78258600-78263400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:78258600-78263400	Weak transcription	Brain Anterior Caudate	brain
8	chr7:78258600-78263600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:78258800-78263400	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:78258800-78263600	Weak transcription	Brain Angular Gyrus	brain
11	chr7:78259000-78263600	Weak transcription	Brain Substantia Nigra	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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