Variant report

Variant	rs11180938
Chromosome Location	chr12:41867237-41867238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GXYLT1-2	chr12:41867167-41867312	ENSG00000257228.1

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10880080	0.97[ASN][1000 genomes]
rs10880084	0.86[ASN][1000 genomes]
rs10880090	0.82[ASN][1000 genomes]
rs11180928	0.96[ASN][1000 genomes]
rs11180932	0.97[ASN][1000 genomes]
rs11180934	0.90[ASN][1000 genomes]
rs11180935	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11180944	1.00[ASN][1000 genomes]
rs11180946	1.00[ASN][1000 genomes]
rs11180947	1.00[ASN][1000 genomes]
rs11180948	1.00[ASN][1000 genomes]
rs11180949	1.00[ASN][1000 genomes]
rs11180950	1.00[ASN][1000 genomes]
rs11180952	1.00[ASN][1000 genomes]
rs11180953	0.97[ASN][1000 genomes]
rs11180957	0.97[ASN][1000 genomes]
rs11180959	0.97[ASN][1000 genomes]
rs11180962	0.97[ASN][1000 genomes]
rs11180963	0.97[ASN][1000 genomes]
rs11180964	0.97[ASN][1000 genomes]
rs11180965	0.97[ASN][1000 genomes]
rs11180966	0.97[ASN][1000 genomes]
rs11180967	0.97[ASN][1000 genomes]
rs11180968	0.97[ASN][1000 genomes]
rs11180969	0.97[ASN][1000 genomes]
rs11180970	0.86[ASN][1000 genomes]
rs11180972	0.86[ASN][1000 genomes]
rs11180973	0.82[ASN][1000 genomes]
rs11180974	0.82[ASN][1000 genomes]
rs11180975	0.82[ASN][1000 genomes]
rs11180976	0.82[ASN][1000 genomes]
rs11180978	0.82[ASN][1000 genomes]
rs12227540	0.82[ASN][1000 genomes]
rs12581707	0.86[ASN][1000 genomes]
rs12582035	0.97[ASN][1000 genomes]
rs1379766	0.97[ASN][1000 genomes]
rs1458172	0.86[ASN][1000 genomes]
rs1458173	0.86[ASN][1000 genomes]
rs17129417	0.97[ASN][1000 genomes]
rs17129436	0.82[ASN][1000 genomes]
rs17835484	0.82[ASN][1000 genomes]
rs2125289	0.86[ASN][1000 genomes]
rs2252312	0.86[ASN][1000 genomes]
rs7968280	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41860200-41869200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41861400-41870000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:41861400-41870400	Weak transcription	Brain Anterior Caudate	brain
4	chr12:41862000-41869800	Weak transcription	Brain Germinal Matrix	brain
5	chr12:41862000-41870200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:41862200-41869400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:41866400-41867400	Active TSS	Fetal Intestine Large	intestine
8	chr12:41866400-41867400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr12:41866400-41867800	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:41866600-41867400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr12:41866800-41870400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:41867000-41867400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr12:41867200-41867600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr12:41867200-41869600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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