Variant report

Variant	rs8041437
Chromosome Location	chr15:50355604-50355605
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11636226	0.81[EUR][1000 genomes]
rs28460885	0.81[EUR][1000 genomes]
rs4405488	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7167956	0.82[AMR][1000 genomes]
rs8025221	0.82[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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
rs8041437	CASC4	cis	cerebellum	SCAN
rs8041437	EIF3J	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50344200-50356600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr15:50348200-50359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr15:50348600-50358600	Weak transcription	Fetal Intestine Large	intestine
4	chr15:50351000-50358400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:50352000-50358400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:50352000-50358600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:50352000-50358600	Weak transcription	Small Intestine	intestine
8	chr15:50352200-50357000	Weak transcription	Colon Smooth Muscle	Colon
9	chr15:50352400-50359400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:50352600-50356400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:50353200-50356800	Weak transcription	Gastric	stomach
12	chr15:50353200-50357800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:50354000-50356400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:50354600-50356000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr15:50354600-50356400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:50354600-50360400	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr15:50355000-50356400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:50355000-50356600	Genic enhancers	Primary hematopoietic stem cells	blood
19	chr15:50355400-50357000	Enhancers	Monocytes-CD14+_RO01746	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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