Variant report

Variant	rs6589833
Chromosome Location	chr11:120561883-120561884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10750176	0.82[CEU][hapmap]
rs10790400	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[MEX][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10790402	0.85[CEU][hapmap]
rs10892618	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10892619	0.84[ASN][1000 genomes]
rs11217974	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11217977	0.84[ASN][1000 genomes]
rs12574240	0.90[EUR][1000 genomes]
rs17245664	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6589831	0.84[CEU][hapmap]
rs6589832	0.85[CEU][hapmap]
rs7105943	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7106140	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7106261	0.96[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7116106	0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7121857	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7122193	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7925270	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs9651696	0.86[CEU][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	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6589833	CD3E	cis	cerebellum	SCAN
rs6589833	TMPRSS13	cis	cerebellum	SCAN
rs6589833	DPAGT1	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120553800-120562400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:120561000-120562000	Enhancers	Fetal Kidney	kidney
3	chr11:120561600-120569200	Weak transcription	Spleen	Spleen
4	chr11:120561800-120565800	Weak transcription	H9 Derived Neuron 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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