Variant report

Variant	rs10896687
Chromosome Location	chr11:57786845-57786846
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1031234	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs1031360	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs12790525	0.84[CEU][hapmap]
rs12799639	0.94[ASN][1000 genomes]
rs1374570	0.90[JPT][hapmap]
rs1376489	0.84[CEU][hapmap]
rs2245676	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs2441950	0.84[ASW][hapmap];0.82[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs2441952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443441	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2514202	0.81[JPT][hapmap]
rs3851121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4509781	0.81[CEU][hapmap]
rs4939180	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs6591450	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7103284	0.89[ASN][1000 genomes]
rs7113760	0.81[CEU][hapmap]
rs7930102	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv328	chr11:57744748-57789940	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv2761678	chr11:57768288-57810886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10896687	PLP1	cis	Brain Pons	GTEx
rs10896687	TIMM10	cis	multi-tissue	Pritchard
rs10896687	OR5M1	cis	cerebellum	SCAN
rs10896687	OR9Q2	cis	cerebellum	SCAN
rs10896687	GLYATL2	cis	parietal	SCAN
rs10896687	UBE2L6	cis	parietal	SCAN
rs10896687	YPEL4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57785800-57791400	Weak transcription	Pancreas	Pancrea
2	chr11:57786000-57787200	Weak transcription	Left Ventricle	heart

Quick Search:

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

what's new

Quick links