Variant report

Variant	rs12540892
Chromosome Location	chr7:14472844-14472845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10237790	0.84[EUR][1000 genomes]
rs10253325	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10264038	0.81[EUR][1000 genomes]
rs10271285	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes]
rs10486031	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs10499440	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs10950525	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10950526	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11525791	1.00[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs11526188	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs11977908	0.85[CEU][hapmap]
rs11978895	1.00[CEU][hapmap]
rs12531006	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12532388	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12532453	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12533433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533729	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12534446	1.00[CEU][hapmap]
rs12538874	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12540646	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12673303	0.93[LWK][hapmap]
rs1367775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1431533	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1431534	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs16878172	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17168175	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17168177	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17168203	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs171926	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17651138	0.85[CEU][hapmap]
rs17651211	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs1835676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1835677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs183808	0.99[EUR][1000 genomes]
rs196750	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs196753	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs196760	1.00[CEU][hapmap]
rs2116317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2116318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2163509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58759714	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59778011	0.99[EUR][1000 genomes]
rs60294470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443273	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9639198	0.85[CEU][hapmap]

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	nsv949033	chr7:14086106-14860323	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv915603	chr7:14443884-14624268	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv1848567	chr7:14464118-14579801	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv971153	chr7:14468435-14473759	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv887707	chr7:14471682-14576163	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12540892	ETV1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:14470600-14473200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:14471800-14473200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:14472400-14473000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:14472400-14473000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:14472400-14473000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:14472600-14473000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:14472600-14473000	Enhancers	Fetal Muscle Leg	muscle

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