Variant report

Variant	rs4540126
Chromosome Location	chr5:60555922-60555923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60555601..60558433-chr5:60563419..60566177,2	K562	blood:
2	chr5:60554941..60557365-chr5:60625053..60627690,3	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10037643	0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs10052765	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10062338	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065444	0.88[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10071763	0.92[ASN][1000 genomes]
rs10434526	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10461467	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10471510	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939892	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs10939893	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs12189420	0.81[AMR][1000 genomes]
rs12189426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518152	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12523278	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs12696979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12696980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696981	0.85[AMR][1000 genomes]
rs12696982	0.87[AMR][1000 genomes]
rs13175564	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs13355792	0.87[AMR][1000 genomes]
rs34439016	0.96[ASN][1000 genomes]
rs35310874	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4315878	1.00[MEX][hapmap]
rs4379148	0.87[AMR][1000 genomes]
rs4400074	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4441832	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4640746	1.00[MEX][hapmap]
rs4699974	0.91[ASN][1000 genomes]
rs4699975	0.91[ASN][1000 genomes]
rs6864367	0.91[ASN][1000 genomes]
rs6867268	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6867417	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6885499	0.91[ASN][1000 genomes]
rs6892128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7448844	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7705381	0.84[AFR][1000 genomes]
rs7737448	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291710	0.85[GIH][hapmap]
rs9291718	0.93[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	esv2760936	chr5:60555229-60556337	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4540126	DEPDC1B	cis	cerebellum	SCAN
rs4540126	RASSF8	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60550400-60573400	Weak transcription	Gastric	stomach
2	chr5:60552600-60557600	Weak transcription	Right Atrium	heart
3	chr5:60553000-60557600	Weak transcription	Stomach Mucosa	stomach
4	chr5:60553800-60557400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:60555800-60556000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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