Variant report

Variant	rs4143837
Chromosome Location	chr15:50406183-50406184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:50406058-50407045	HL-60	blood:	n/a	n/a

Variant related genes	Relation type
ATP8B4	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519259	0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11070747	0.91[JPT][hapmap]
rs11857230	0.91[JPT][hapmap]
rs12050709	0.81[JPT][hapmap]
rs12148444	0.85[JPT][hapmap]
rs2414018	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs28416764	0.93[ASN][1000 genomes]
rs2899454	0.86[ASN][1000 genomes]
rs3985833	0.97[ASN][1000 genomes]
rs41362650	0.85[JPT][hapmap]
rs4775851	0.91[JPT][hapmap]
rs56216064	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62021719	0.92[ASN][1000 genomes]
rs6493402	0.91[JPT][hapmap]
rs7168944	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7170781	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7172615	0.81[JPT][hapmap]
rs7172916	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7173633	0.88[ASN][1000 genomes]
rs7177318	0.85[JPT][hapmap]
rs8040030	0.91[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4143837	PCDHB13	trans	parietal	SCAN
rs4143837	ATP8B4	cis	parietal	SCAN
rs4143837	VAMP3	trans	parietal	SCAN
rs4143837	ARMC6	trans	parietal	SCAN
rs4143837	C15orf33	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50399200-50407200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:50399800-50407800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:50402200-50406400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:50402600-50407800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr15:50403400-50409000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr15:50403600-50409000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:50403800-50411200	Weak transcription	Thymus	Thymus
8	chr15:50404400-50406800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
9	chr15:50405600-50410800	Weak transcription	K562	blood
10	chr15:50405800-50406400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:50406000-50406200	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr15:50406000-50408800	Flanking Active TSS	Primary hematopoietic stem cells	blood

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