Variant report

Variant	rs11161729
Chromosome Location	chr1:86551864-86551865
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10873746	0.84[EUR][1000 genomes]
rs11161732	0.84[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs11161733	0.82[EUR][1000 genomes]
rs12728287	0.83[EUR][1000 genomes]
rs1507281	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs36035589	0.83[EUR][1000 genomes]
rs6665375	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1797916	chr1:86529538-86556298	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1803171	chr1:86551864-86556298	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11161729	RPF1	cis	parietal	SCAN
rs11161729	COL24A1	cis	lymphoblastoid	seeQTL
rs11161729	COL24A1	cis	Artery Tibial	GTEx
rs11161729	LRRC8D	cis	cerebellum	SCAN
rs11161729	WDR63	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86547000-86556800	Weak transcription	Pancreas	Pancrea
2	chr1:86547400-86553600	Weak transcription	Fetal Lung	lung
3	chr1:86550600-86552400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:86550800-86552200	Enhancers	Primary hematopoietic stem cells	blood
5	chr1:86550800-86552200	Enhancers	Dnd41	blood
6	chr1:86550800-86570400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:86551000-86552000	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:86551200-86552200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:86551200-86552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:86551400-86552000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:86551800-86552000	Flanking Active TSS	GM12878-XiMat	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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