Variant report

Variant	rs17554587
Chromosome Location	chr15:46036450-46036451
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1033167	0.93[ASN][1000 genomes]
rs1356881	0.86[ASN][1000 genomes]
rs1949575	0.88[ASN][1000 genomes]
rs2244179	0.86[ASN][1000 genomes]
rs2413788	0.86[ASN][1000 genomes]
rs2460628	0.86[ASN][1000 genomes]
rs2460629	0.85[ASN][1000 genomes]
rs2460630	0.85[ASN][1000 genomes]
rs2460631	0.86[ASN][1000 genomes]
rs2460632	0.85[ASN][1000 genomes]
rs2460638	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28829710	0.93[ASN][1000 genomes]
rs28855819	0.93[ASN][1000 genomes]
rs939423	0.80[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	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv523136	chr15:45990780-46158407	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1041692	chr15:46017726-46048854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	n/a	n/a	inside rSNPs	n/a
5	nsv1524	chr15:46030486-46061021	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17554587	TYRO3	cis	parietal	SCAN
rs17554587	NDUFAF1	cis	parietal	SCAN
rs17554587	THBS1	cis	parietal	SCAN
rs17554587	DUOX2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:46035000-46036600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr15:46035000-46037000	Enhancers	Rectal Smooth Muscle	rectum
3	chr15:46035000-46040200	Enhancers	Fetal Brain Male	brain
4	chr15:46035400-46036600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr15:46035800-46036600	Flanking Active TSS	Fetal Brain Female	brain
6	chr15:46035800-46036600	Enhancers	Fetal Kidney	kidney
7	chr15:46036200-46038000	Enhancers	Brain Germinal Matrix	brain
8	chr15:46036400-46036600	Flanking Active TSS	Colon Smooth Muscle	Colon

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Input of quick search could be:

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

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