Variant report

Variant	rs12123862
Chromosome Location	chr1:56836116-56836117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10888967	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11206795	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11206798	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12120414	0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs12135708	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12143053	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561840	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562353	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12563015	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12566944	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12567196	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567652	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1931076	0.83[MEX][hapmap]
rs28784046	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28819096	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35691565	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4279887	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4397689	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421626	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4462192	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4477326	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4564188	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600084	0.83[MEX][hapmap]
rs4912223	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912230	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912409	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4912412	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4912413	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61772736	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588619	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6588622	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6588623	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6680675	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6684867	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515200	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518559	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7526379	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7527370	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529732	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529741	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542209	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7542690	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550046	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932	chr1:56816732-56842261	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv3344758	chr1:56830514-56836162	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv508204	chr1:56830844-56840857	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
4	esv1005520	chr1:56831042-56839645	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12123862	LRP8	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56825400-56839000	Weak transcription	Psoas Muscle	Psoas
2	chr1:56835000-56836200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:56835400-56836200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr1:56835600-56836200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:56835600-56837000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr1:56835600-56837200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:56835800-56837000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:56835800-56837200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:56835800-56837200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:56835800-56837200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:56836000-56836200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:56836000-56836200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:56836000-56836200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:56836000-56836600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:56836000-56836800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:56836000-56836800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr1:56836000-56836800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:56836000-56837000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:56836000-56837200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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