Variant report

Variant	rs12741793
Chromosome Location	chr1:75678584-75678585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11162738	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11162810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162944	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1144297	0.88[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1144298	0.85[EUR][1000 genomes]
rs12039281	0.84[ASN][1000 genomes]
rs12042874	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12044451	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249655	0.95[CEU][hapmap]
rs1394736	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1700893	0.87[CEU][hapmap]
rs1948874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202473	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs599291	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs600734	0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs609574	0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs611899	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs615372	0.91[ASN][1000 genomes]
rs627494	0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs642145	0.91[ASN][1000 genomes]
rs645287	0.91[ASN][1000 genomes]
rs6689909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686453	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs687715	0.85[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7516812	0.85[EUR][1000 genomes]
rs7534079	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs975152	0.85[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[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	nsv871743	chr1:75235082-75714554	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12741793	ETV3L	trans	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75671200-75678600	Weak transcription	Brain Germinal Matrix	brain
2	chr1:75675000-75679400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:75676400-75700400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:75677400-75686200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:75678400-75678800	Strong transcription	Fetal Brain Female	brain

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