Variant report

Variant	rs11180905
Chromosome Location	chr12:41805377-41805378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GXYLT1-2	chr12:41805327-41805677	ENSG00000257228.1

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10748302	0.82[YRI][hapmap]
rs10880077	1.00[YRI][hapmap]
rs11180853	1.00[YRI][hapmap]
rs11180857	1.00[YRI][hapmap]
rs11180858	1.00[YRI][hapmap]
rs11180861	1.00[YRI][hapmap]
rs11180865	1.00[YRI][hapmap]
rs11180880	1.00[YRI][hapmap]
rs11180881	1.00[YRI][hapmap]
rs11180888	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11180898	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11180907	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11180908	1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11180912	1.00[CEU][hapmap]
rs11180914	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12296173	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12298084	0.82[YRI][hapmap]
rs12305552	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12308926	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12312032	1.00[CEU][hapmap]
rs12318761	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12321550	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12322196	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1918224	1.00[CEU][hapmap]
rs285585	1.00[CEU][hapmap]
rs4558215	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74077600	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74078808	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74078810	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74078819	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9652046	1.00[YRI][hapmap]
rs987823	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
13	nsv1050627	chr12:41789891-41809009	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41802800-41808600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:41804800-41808400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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