Variant report

Variant	rs4564799
Chromosome Location	chr2:76981827-76981828
allele	C/T
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:16)

rs_ID	r²[population]
rs10186864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11126561	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]
rs12713881	0.83[CHB][hapmap]
rs12713882	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13014978	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1400848	0.95[CEU][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1400849	0.95[CEU][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1517778	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1517779	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1517780	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2222178	0.95[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2222179	1.00[CEU][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2222180	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];0.95[JPT][hapmap]
rs7563920	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608234	0.92[YRI][hapmap]

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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4564799	TTC31	cis	parietal	SCAN
rs4564799	MRPL19	cis	cerebellum	SCAN
rs4564799	ACTG2	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	chr2:76981600-76982200	Enhancers	Gastric	stomach
6	chr2:76981800-76982000	Enhancers	H9 Cell Line	embryonic stem cell
7	chr2:76981800-76982200	Enhancers	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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