Variant report

Variant	rs17740607
Chromosome Location	chr15:50555544-50555545
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10518836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11856059	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11857173	0.88[ASN][1000 genomes]
rs17509944	1.00[ASW][hapmap]
rs17740669	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17796788	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72737093	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17740607	SLC24A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50548000-50555600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr15:50548200-50555800	Enhancers	Primary hematopoietic stem cells	blood
3	chr15:50550200-50555600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:50550800-50556000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr15:50551400-50555800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr15:50551800-50555600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr15:50553200-50555600	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr15:50553400-50555600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:50553400-50555800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:50554200-50555600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr15:50554200-50555600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr15:50554200-50555600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr15:50554200-50555800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr15:50554400-50555600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:50554400-50555600	Enhancers	GM12878-XiMat	blood
16	chr15:50554800-50555600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr15:50555200-50555600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr15:50555200-50556400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:50555400-50579400	Weak transcription	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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