Variant report

Variant	rs2778902
Chromosome Location	chr9:101332459-101332460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1167765	0.88[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1167766	0.86[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.83[TSI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1167767	0.80[ASW][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1167768	0.86[ASW][hapmap];0.96[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1183825	0.85[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1186363	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1622942	0.94[JPT][hapmap]
rs16917171	0.91[YRI][hapmap]
rs2259639	0.85[TSI][hapmap]
rs867762	0.91[YRI][hapmap]
rs944686	0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv831665	chr9:101170061-101367692	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv6633	chr9:101308371-101342811	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv1040325	chr9:101328103-101354107	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv466438	chr9:101328200-101361584	Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv614949	chr9:101328200-101361584	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2778902	XPA	cis	parietal	SCAN
rs2778902	FOXE1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101325800-101333000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:101328200-101332800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:101331600-101334000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:101332200-101334800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:101332400-101333000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr9:101332400-101333600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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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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