Variant report

Variant	rs1400848
Chromosome Location	chr2:76987268-76987269
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10186864	0.95[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11126561	0.95[CEU][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12713882	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13014978	0.95[CEU][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1400849	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1517778	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1517779	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1517780	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2222178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2222179	0.95[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs2222180	0.95[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs4564799	0.95[CEU][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6730015	0.95[CEU][hapmap]
rs7563920	0.95[CEU][hapmap];0.85[MEX][hapmap];0.85[AMR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1400848	ACTG2	cis	cerebellum	SCAN
rs1400848	MRPL19	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:76973400-76989200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:76979400-76988200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:76984200-76988600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:76985800-76988000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:76986200-76988200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:76986600-76987600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:76986600-76987600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:76986600-76988000	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:76987000-76987800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:76987200-76987600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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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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