Variant report

Variant	rs1286170
Chromosome Location	chr11:59831930-59831931
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:15)

rs_ID	r²[population]
rs1151104	0.92[JPT][hapmap]
rs1151105	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1286169	0.92[JPT][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1286289	0.80[CEU][hapmap]
rs1296390	0.80[AMR][1000 genomes]
rs3016835	0.80[AMR][1000 genomes]
rs474951	0.88[ASW][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs501697	0.88[ASW][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs525828	0.82[AFR][1000 genomes]
rs528823	0.88[ASW][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs539360	0.92[JPT][hapmap];0.85[AFR][1000 genomes]
rs543695	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs558678	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs558788	0.83[CHD][hapmap];0.92[JPT][hapmap]
rs579721	0.92[JPT][hapmap]

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	nsv832173	chr11:59788884-59940560	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv468579	chr11:59814287-59975400	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv555150	chr11:59814287-59975400	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1286170	C11orf9	cis	parietal	SCAN
rs1286170	POLR2G	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59822800-59832000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:59831200-59832200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59831200-59832400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:59831200-59832400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr11:59831200-59833000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:59831600-59832000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:59831600-59832200	Enhancers	Primary B cells from cord blood	blood
8	chr11:59831600-59832600	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr11:59831800-59832400	Enhancers	K562	blood

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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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