Variant report

Variant	rs2953802
Chromosome Location	chr8:8851881-8851882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1045529	0.85[CEU][hapmap]
rs17701675	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1964356	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288671	0.89[CEU][hapmap];0.85[MEX][hapmap]
rs2288673	0.83[AMR][1000 genomes]
rs2915251	0.89[CEU][hapmap]
rs2956244	0.84[CEU][hapmap]
rs2979247	0.81[CEU][hapmap]
rs2979256	0.89[CEU][hapmap]
rs2979265	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs4841075	0.90[JPT][hapmap]
rs4841077	0.90[JPT][hapmap];0.86[MEX][hapmap]
rs4841083	0.88[CEU][hapmap]
rs6987558	0.89[CEU][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes]
rs6993244	0.82[AMR][1000 genomes]
rs7015336	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv831229	chr8:8751523-8926235	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv610205	chr8:8799111-8891644	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	n/a

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2953802	MFHAS1	cis	cerebellum	SCAN
rs2953802	CTSB	cis	cerebellum	SCAN
rs2953802	DEFB136	cis	parietal	SCAN
rs2953802	PRSS55	cis	cerebellum	SCAN
rs2953802	PPP1R3B	cis	cerebellum	SCAN
rs2953802	BLK	Cis_chr	lymphoblastoid	RTeQTL
rs2953802	C8orf5	Cis_chr	lymphoblastoid	RTeQTL
rs2953802	THEX1	Cis_1M	lymphoblastoid	RTeQTL
rs2953802	DEFB134	cis	cerebellum	SCAN
rs2953802	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8846600-8859800	Weak transcription	Brain Anterior Caudate	brain
2	chr8:8847000-8852000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr8:8848600-8852000	Weak transcription	Fetal Intestine Large	intestine
4	chr8:8848600-8852600	Weak transcription	HepG2	liver
5	chr8:8848800-8852400	Weak transcription	Liver	Liver
6	chr8:8851800-8852800	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr8:8851800-8853200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
8	chr8:8851800-8853400	Enhancers	Primary monocytes fromperipheralblood	blood

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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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