Variant report

Variant	rs11139955
Chromosome Location	chr9:85813385-85813386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10867954	0.85[CHD][hapmap]
rs11139954	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11139959	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11139965	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11139971	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11139973	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11139975	0.94[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11139976	0.81[CHD][hapmap]
rs11139978	0.85[CHD][hapmap];0.81[GIH][hapmap]
rs11139983	0.85[CHD][hapmap];0.81[GIH][hapmap]
rs1323772	0.94[CEU][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17400361	0.94[CEU][hapmap];0.92[CHB][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4877745	0.81[CHD][hapmap]
rs58862231	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7848774	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831642	chr9:85679425-85817338	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85811800-85813400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:85811800-85813600	Enhancers	Fetal Heart	heart
3	chr9:85812000-85813400	Enhancers	Brain Germinal Matrix	brain
4	chr9:85812200-85813600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:85812400-85813400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr9:85812400-85813400	Weak transcription	Fetal Brain Male	brain
7	chr9:85812400-85813600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:85812600-85815000	Enhancers	Fetal Stomach	stomach
9	chr9:85813200-85813400	Flanking Active TSS	Fetal Brain Female	brain
10	chr9:85813200-85813600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr9:85813200-85813600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr9:85813200-85813600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr9:85813200-85813800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:85813200-85813800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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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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