Variant report

Variant	rs41362650
Chromosome Location	chr15:50369375-50369376
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	chr15:50368228..50370231-chr15:50409424..50412316,2	MCF-7	breast:
2	chr15:50366775..50369568-chr15:50372000..50374396,2	K562	blood:

Variant related genes	Relation type
ENSG00000104043	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10519257	0.95[CEU][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11070745	0.95[ASN][1000 genomes]
rs11070747	0.94[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11070748	0.84[ASN][1000 genomes]
rs11857230	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12050709	0.95[CEU][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12148444	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs12441604	0.86[ASN][1000 genomes]
rs12442280	0.84[ASN][1000 genomes]
rs12902530	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903325	0.90[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12905011	0.90[EUR][1000 genomes]
rs12909131	1.00[ASW][hapmap];0.89[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2414016	0.86[ASN][1000 genomes]
rs2414018	0.81[JPT][hapmap]
rs28369108	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34970637	0.88[EUR][1000 genomes]
rs4143837	0.85[JPT][hapmap]
rs4775849	0.94[ASN][1000 genomes]
rs4775851	0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4775852	0.86[ASN][1000 genomes]
rs6493402	0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs68191015	0.81[EUR][1000 genomes]
rs7168944	0.81[JPT][hapmap]
rs7170781	0.81[JPT][hapmap]
rs7170947	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7172615	0.89[CEU][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172916	0.81[JPT][hapmap]
rs7177318	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7178944	0.86[ASN][1000 genomes]
rs7179392	0.96[ASN][1000 genomes]
rs8040030	0.84[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8040357	0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41362650	ATP8B4	cis	cerebellum	SCAN
rs41362650	ATP8B4	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50367200-50369800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr15:50367200-50380600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr15:50367400-50381600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr15:50368000-50370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:50368000-50380800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr15:50368800-50370400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:50368800-50370600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:50368800-50371000	Enhancers	Colon Smooth Muscle	Colon
9	chr15:50369000-50370200	Enhancers	Fetal Intestine Large	intestine
10	chr15:50369000-50370200	Enhancers	Rectal Smooth Muscle	rectum
11	chr15:50369000-50370600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:50369000-50371000	Enhancers	Primary hematopoietic stem cells	blood
13	chr15:50369200-50369800	Enhancers	Brain Anterior Caudate	brain
14	chr15:50369200-50370000	Enhancers	NHDF-Ad	bronchial
15	chr15:50369200-50370600	Enhancers	Brain Substantia Nigra	brain
16	chr15:50369200-50371200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood

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