Variant report

Variant	rs12089049
Chromosome Location	chr1:186627209-186627210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10798049	0.85[ASN][1000 genomes]
rs10911883	0.85[ASN][1000 genomes]
rs10911884	0.85[ASN][1000 genomes]
rs10911885	0.85[ASN][1000 genomes]
rs10911887	0.85[ASN][1000 genomes]
rs10911889	0.85[ASN][1000 genomes]
rs10911900	0.83[EUR][1000 genomes]
rs10911901	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911903	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911907	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911908	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911909	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911910	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10911911	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1119066	0.84[ASN][1000 genomes]
rs1119230	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1119231	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11583191	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11584118	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585033	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11585801	0.85[ASN][1000 genomes]
rs12057695	0.85[ASN][1000 genomes]
rs12061722	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12062679	0.85[ASN][1000 genomes]
rs12064238	0.84[ASN][1000 genomes]
rs12076624	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12077211	0.85[ASN][1000 genomes]
rs12084433	0.84[ASN][1000 genomes]
rs12085848	0.85[ASN][1000 genomes]
rs12089127	0.85[ASN][1000 genomes]
rs12097208	0.85[ASN][1000 genomes]
rs12401885	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12402603	0.83[EUR][1000 genomes]
rs12402766	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12402797	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12403185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12405141	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12405541	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12405919	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12408222	0.85[ASN][1000 genomes]
rs12408912	0.85[ASN][1000 genomes]
rs12409744	0.84[ASN][1000 genomes]
rs12410549	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1474596	0.81[ASN][1000 genomes]
rs1569879	0.85[ASN][1000 genomes]
rs17520924	0.85[ASN][1000 genomes]
rs1997977	0.85[ASN][1000 genomes]
rs2038225	0.85[ASN][1000 genomes]
rs20417	0.93[ASN][1000 genomes]
rs20432	0.84[ASN][1000 genomes]
rs2066826	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143416	0.84[ASN][1000 genomes]
rs2143417	0.84[ASN][1000 genomes]
rs2179555	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2383511	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2383515	0.84[ASN][1000 genomes]
rs2383516	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383529	0.84[ASN][1000 genomes]
rs28469836	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34975495	0.85[ASN][1000 genomes]
rs4422959	0.84[ASN][1000 genomes]
rs4648250	0.96[ASN][1000 genomes]
rs4648276	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648306	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648308	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59665821	0.85[ASN][1000 genomes]
rs60203808	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61532952	1.00[ASN][1000 genomes]
rs6425033	0.85[ASN][1000 genomes]
rs66494422	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665419	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6666199	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66850891	0.85[ASN][1000 genomes]
rs6685280	0.84[ASN][1000 genomes]
rs6690318	0.85[ASN][1000 genomes]
rs6698048	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67143595	0.85[ASN][1000 genomes]
rs67203540	0.85[ASN][1000 genomes]
rs67362011	0.85[ASN][1000 genomes]
rs67607835	0.85[ASN][1000 genomes]
rs67804662	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67816471	0.83[EUR][1000 genomes]
rs68096880	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689465	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72721517	0.85[ASN][1000 genomes]
rs72721521	0.85[ASN][1000 genomes]
rs72721544	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72721568	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73052465	0.85[ASN][1000 genomes]
rs7512750	0.85[ASN][1000 genomes]
rs7522862	0.85[ASN][1000 genomes]
rs7533973	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538407	0.85[ASN][1000 genomes]
rs7542810	0.85[ASN][1000 genomes]
rs7545438	0.85[ASN][1000 genomes]
rs7548600	0.85[ASN][1000 genomes]
rs964571	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9659276	0.85[ASN][1000 genomes]
rs9783017	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783052	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9804178	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186621800-186630400	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:186625000-186628200	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:186625400-186628000	Weak transcription	HUVEC	blood vessel
4	chr1:186625400-186630400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:186626600-186629200	Enhancers	Hela-S3	cervix
6	chr1:186626600-186629200	Enhancers	HMEC	breast
7	chr1:186626600-186629600	Enhancers	NHEK	skin
8	chr1:186626800-186629600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:186626800-186632800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:186627200-186628400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:186627200-186629600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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