Variant report

Variant	rs17483139
Chromosome Location	chr15:50004512-50004513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10519233	0.94[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329455	0.94[CEU][hapmap];0.91[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354918	1.00[ASN][1000 genomes]
rs1588127	0.94[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17402569	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17404262	0.88[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17480434	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17481696	0.94[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28465200	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28516445	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568399	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635979	1.00[ASN][1000 genomes]
rs28671247	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798135	1.00[ASN][1000 genomes]
rs28843724	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210227	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9920033	1.00[YRI][hapmap]
rs9920574	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920705	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv569393	chr15:49977687-50012256	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17483139	TNFAIP8L3	cis	parietal	SCAN
rs17483139	TRPM7	cis	cerebellum	SCAN
rs17483139	DTWD1	cis	cerebellum	SCAN
rs17483139	CEP152	cis	cerebellum	SCAN
rs17483139	SECISBP2L	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50003800-50010400	Weak transcription	Aorta	Aorta
2	chr15:50004200-50004600	Active TSS	Stomach Smooth Muscle	stomach
3	chr15:50004200-50004800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr15:50004200-50004800	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr15:50004200-50005000	Enhancers	Brain Cingulate Gyrus	brain
6	chr15:50004400-50011600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr15:50004400-50014200	Enhancers	Primary monocytes fromperipheralblood	blood

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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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