Variant report

Variant	rs7939568
Chromosome Location	chr11:8442054-8442055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1011858	0.83[ASN][1000 genomes]
rs10840032	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840033	1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10840037	0.94[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11041904	0.81[ASN][1000 genomes]
rs11041912	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11041927	0.82[CHB][hapmap]
rs11041939	0.81[JPT][hapmap]
rs11041943	0.80[JPT][hapmap]
rs11041966	0.81[JPT][hapmap]
rs12222273	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12224971	0.82[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12226334	0.83[ASN][1000 genomes]
rs12284461	1.00[ASN][1000 genomes]
rs12363733	0.83[ASN][1000 genomes]
rs12576010	1.00[ASN][1000 genomes]
rs12576952	1.00[ASN][1000 genomes]
rs2311435	0.94[ASN][1000 genomes]
rs4586148	0.82[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs59645839	1.00[ASN][1000 genomes]
rs73402046	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7929310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	esv1797209	chr11:8417452-8474015	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7939568	OR52W1	cis	parietal	SCAN
rs7939568	OR51L1	cis	cerebellum	SCAN
rs7939568	LMO1	cis	cerebellum	SCAN
rs7939568	STK33	cis	cerebellum	SCAN
rs7939568	LMO1	cis	parietal	SCAN
rs7939568	LYVE1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8426600-8447200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:8429600-8451200	Weak transcription	Fetal Heart	heart
3	chr11:8431400-8447000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:8431400-8447400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:8435000-8449000	Weak transcription	Psoas Muscle	Psoas
6	chr11:8439200-8447600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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