Variant report

Variant	rs2225153
Chromosome Location	chr1:167003579-167003580
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1410247	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2025893	0.98[ASN][1000 genomes]
rs393025	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs402031	0.81[ASN][1000 genomes]
rs4657621	0.98[ASN][1000 genomes]
rs6427051	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs6661553	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6667210	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6693185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs6694465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6698931	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[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	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv528049	chr1:167003539-167010083	Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv519114	chr1:167003539-167015184	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2225153	GPA33	cis	multi-tissue	Pritchard
rs2225153	TMCO1	cis	parietal	SCAN
rs2225153	MAEL	cis	parietal	SCAN
rs2225153	MAEL	cis	lymphoblastoid	seeQTL
rs2225153	GPR161	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:167002800-167003600	Enhancers	Liver	Liver
2	chr1:167003400-167003800	Flanking Active TSS	Fetal Heart	heart

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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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