Variant report

Variant	rs8040030
Chromosome Location	chr15:50376587-50376588
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:50371975..50373959-chr15:50374095..50376728,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10519257	0.86[JPT][hapmap]
rs10519259	0.81[JPT][hapmap]
rs11070745	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070747	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11070748	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11638799	0.81[JPT][hapmap]
rs11638841	0.83[JPT][hapmap]
rs11857230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12050709	0.91[JPT][hapmap]
rs12148444	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441604	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12442280	0.88[ASN][1000 genomes]
rs12902530	0.95[ASN][1000 genomes]
rs12915042	0.81[JPT][hapmap]
rs2414016	0.91[ASN][1000 genomes]
rs2414018	0.86[JPT][hapmap]
rs28369108	0.95[ASN][1000 genomes]
rs41362650	0.84[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4143837	0.91[JPT][hapmap]
rs4775849	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4775851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4775852	0.91[ASN][1000 genomes]
rs6493402	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7168944	0.85[JPT][hapmap]
rs7170781	0.86[JPT][hapmap]
rs7170947	0.86[JPT][hapmap]
rs7172615	0.91[JPT][hapmap]
rs7172916	0.86[JPT][hapmap]
rs7177318	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178944	0.91[ASN][1000 genomes]
rs7179392	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040357	0.89[ASN][1000 genomes]

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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8040030	CASC4	cis	parietal	SCAN
rs8040030	EID1	cis	parietal	SCAN
rs8040030	ATP8B4	cis	parietal	SCAN
rs8040030	ATP8B4	cis	multi-tissue	Pritchard

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50367200-50380600	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr15:50367400-50381600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr15:50368000-50380800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr15:50373800-50377000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:50373800-50377800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:50374400-50378000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:50375000-50376600	Enhancers	NHDF-Ad	bronchial
8	chr15:50375000-50377600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:50375200-50377400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:50376200-50376800	Genic enhancers	Primary hematopoietic stem cells	blood

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