Variant report

Variant	rs11180882
Chromosome Location	chr12:41784997-41784998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10506193	1.00[CHB][hapmap]
rs10880089	1.00[CHB][hapmap]
rs10880091	1.00[CHB][hapmap]
rs10880093	1.00[CHB][hapmap]
rs10880095	1.00[CHB][hapmap]
rs10880096	1.00[CHB][hapmap]
rs11180567	1.00[JPT][hapmap]
rs11180586	1.00[JPT][hapmap]
rs11180587	1.00[JPT][hapmap]
rs11180626	1.00[JPT][hapmap]
rs11180646	1.00[JPT][hapmap]
rs11180839	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180853	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180979	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11180981	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs11180984	1.00[CHB][hapmap]
rs12227680	1.00[CHB][hapmap]
rs12229610	1.00[CHB][hapmap]
rs12230775	1.00[CHB][hapmap]
rs12296962	1.00[JPT][hapmap]
rs12297322	1.00[JPT][hapmap]
rs12300590	1.00[JPT][hapmap]
rs12300840	1.00[JPT][hapmap]
rs12300953	1.00[JPT][hapmap]
rs12302094	1.00[JPT][hapmap]
rs12305125	1.00[JPT][hapmap]
rs12305252	1.00[JPT][hapmap]
rs12307937	1.00[JPT][hapmap]
rs12310793	1.00[JPT][hapmap]
rs12315362	1.00[JPT][hapmap]
rs12315979	1.00[JPT][hapmap]
rs12317394	1.00[JPT][hapmap]
rs12427081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1350431	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1367606	1.00[JPT][hapmap]
rs1379767	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs1431126	1.00[JPT][hapmap]
rs1458169	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1551594	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1589983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17129202	1.00[JPT][hapmap]
rs17129211	1.00[JPT][hapmap]
rs17129291	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1902908	1.00[CHB][hapmap]
rs1918231	1.00[JPT][hapmap]
rs2054211	1.00[CHB][hapmap]
rs2082222	1.00[JPT][hapmap]
rs2217492	1.00[JPT][hapmap]
rs2733272	1.00[CHB][hapmap]
rs2733273	1.00[CHB][hapmap]
rs2733294	1.00[CHB][hapmap]
rs285586	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs285587	1.00[CHB][hapmap]
rs3110389	1.00[CHB][hapmap]
rs3858730	1.00[JPT][hapmap]
rs4768004	1.00[JPT][hapmap];0.82[MKK][hapmap]
rs7486754	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
2	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv899036	chr12:41777144-41807859	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv899037	chr12:41777144-41819215	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv1044910	chr12:41778831-41813198	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
6	esv2761735	chr12:41780758-41811938	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
7	esv2757501	chr12:41780758-41816002	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
8	esv2759896	chr12:41780758-41816002	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv2755020	chr12:41780758-41820936	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
10	nsv899038	chr12:41784137-41819215	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
11	nsv818915	chr12:41784997-41811063	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a
12	nsv899039	chr12:41784997-41813207	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11180882	PDZRN4	cis	parietal	SCAN
rs11180882	DPY19L4	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41776200-41787400	Weak transcription	Aorta	Aorta
2	chr12:41784400-41785000	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links