Variant report

Variant	rs11126561
Chromosome Location	chr2:76982546-76982547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10186864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12713881	0.83[CHB][hapmap]
rs12713882	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13014978	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1400848	0.95[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1400849	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1517778	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1517779	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs1517780	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2222178	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2222179	1.00[CEU][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes]
rs2222180	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]
rs4564799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6730015	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs7563920	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes];0.83[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	nsv458263	chr2:76976626-76994984	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11126561	ACTG2	cis	cerebellum	SCAN
rs11126561	TTC31	cis	parietal	SCAN
rs11126561	MRPL19	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:76963800-76985800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:76973400-76989200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:76974800-76986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:76979400-76988200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:76982000-76986400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:76982200-76984200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:76982200-76984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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