Variant report

Variant	rs12640378
Chromosome Location	chr4:85950122-85950123
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10029496	0.82[EUR][1000 genomes]
rs10856851	0.84[EUR][1000 genomes]
rs10856852	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097026	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11097030	0.94[ASN][1000 genomes]
rs11730981	0.85[EUR][1000 genomes]
rs11732309	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732347	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498637	0.83[EUR][1000 genomes]
rs12498787	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12503215	0.86[EUR][1000 genomes]
rs12503330	0.84[EUR][1000 genomes]
rs12506456	0.85[EUR][1000 genomes]
rs12510410	0.87[EUR][1000 genomes]
rs12640811	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12648852	0.85[EUR][1000 genomes]
rs13109918	0.85[EUR][1000 genomes]
rs13114115	0.83[EUR][1000 genomes]
rs13118671	0.86[TSI][hapmap]
rs13124246	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13141072	0.81[EUR][1000 genomes]
rs13141322	0.83[EUR][1000 genomes]
rs13148035	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1508670	0.85[JPT][hapmap]
rs17009317	0.84[TSI][hapmap]
rs17009341	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs2046404	0.91[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2869216	0.84[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap]
rs28754901	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34239067	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34314581	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4131745	0.83[EUR][1000 genomes]
rs4287999	0.95[ASN][1000 genomes]
rs4376130	0.87[EUR][1000 genomes]
rs4383611	0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs4470615	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4533765	0.87[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4590017	0.82[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap]
rs4624645	0.87[EUR][1000 genomes]
rs4626191	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4634212	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56094216	0.82[EUR][1000 genomes]
rs56194765	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531777	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6531782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531783	0.82[CEU][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs66965560	0.83[EUR][1000 genomes]
rs6833661	0.83[EUR][1000 genomes]
rs6847811	0.87[EUR][1000 genomes]
rs72664952	0.84[EUR][1000 genomes]
rs7654035	0.91[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs7661609	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7663580	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7675324	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7682896	0.80[EUR][1000 genomes]
rs7692223	0.82[CEU][hapmap];0.91[JPT][hapmap]
rs7694949	0.91[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs7699226	0.91[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs9684737	0.86[EUR][1000 genomes]
rs9790649	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3367963	chr4:85911017-86246036	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12640378	BC038746	cis	multi-tissue	Pritchard
rs12640378	NCRNA00247	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85949600-85950200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:85949600-85950400	Enhancers	NHDF-Ad	bronchial
3	chr4:85949600-85950600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:85950000-85950400	Enhancers	Osteobl	bone
5	chr4:85950000-85950600	Enhancers	HSMM	muscle
6	chr4:85950000-85950600	Enhancers	HSMMtube	muscle

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