Variant report

Variant	rs2222180
Chromosome Location	chr2:76997161-76997162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10186864	1.00[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11126561	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713882	1.00[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs13014978	1.00[CEU][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs1400848	0.95[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs1400849	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs1517778	0.93[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1517779	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1517780	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2222178	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs2222179	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4564799	1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6730015	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs7563920	1.00[CEU][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv582235	chr2:76881210-76997763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv874320	chr2:76971709-77013724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	nsv1011401	chr2:76982546-77068714	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv999822	chr2:76994539-77022762	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2222180	ACTG2	cis	cerebellum	SCAN
rs2222180	MRPL19	cis	cerebellum	SCAN
rs2222180	TTC31	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:76988000-76998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:76994600-76998000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:76996600-76997200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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