Variant report

Variant	rs13138813
Chromosome Location	chr4:47425933-47425934
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	chr4:47425451..47428331-chr4:47428663..47430199,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10004682	0.91[ASN][1000 genomes]
rs10022793	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10029474	0.91[ASN][1000 genomes]
rs10030377	1.00[CEU][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10155173	0.88[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10155287	0.88[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs10155404	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10938484	0.91[ASN][1000 genomes]
rs11724538	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11729717	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11944531	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13102764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13106855	0.81[CEU][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs28457819	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28625886	0.91[ASN][1000 genomes]
rs28631883	0.91[ASN][1000 genomes]
rs4356892	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4388055	0.91[ASN][1000 genomes]
rs4446282	0.91[ASN][1000 genomes]
rs4450898	0.91[ASN][1000 genomes]
rs4493516	0.88[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes]
rs4591574	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4635794	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4695232	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57163868	0.91[ASN][1000 genomes]
rs61003073	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6822230	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6836637	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664913	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7671396	0.87[ASN][1000 genomes]
rs7693987	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7699557	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9942270	0.91[ASN][1000 genomes]
rs9998407	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[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	nsv998919	chr4:47207023-47476876	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv879005	chr4:47408838-47548254	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13138813	ATP10D	Cis_1M	lymphoblastoid	RTeQTL
rs13138813	CORIN	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47404000-47439000	Weak transcription	Brain Anterior Caudate	brain
2	chr4:47425400-47433000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:47425800-47426800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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