Variant report

Variant	rs6488259
Chromosome Location	chr12:10252509-10252510
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10772231	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10772234	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845032	0.90[EUR][1000 genomes]
rs10845035	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10845037	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845039	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10845041	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11053577	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11053578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053580	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11053581	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300167	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12370211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372259	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1352477	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1387140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1948184	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1948185	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2087304	0.92[ASN][1000 genomes]
rs2087305	0.92[ASN][1000 genomes]
rs2087306	0.89[ASN][1000 genomes]
rs2087307	0.98[ASN][1000 genomes]
rs2220436	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2277416	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306891	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306892	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306893	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306894	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2401600	0.98[ASN][1000 genomes]
rs2401601	0.98[ASN][1000 genomes]
rs2401602	0.96[ASN][1000 genomes]
rs2401603	0.96[ASN][1000 genomes]
rs2401604	0.98[ASN][1000 genomes]
rs2401605	0.98[ASN][1000 genomes]
rs2401606	0.98[ASN][1000 genomes]
rs2401607	0.98[ASN][1000 genomes]
rs2401611	0.81[ASN][1000 genomes]
rs2401614	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401615	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2401616	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3825300	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886137	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3887490	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3912644	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3912645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3994131	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3994132	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4265666	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4499082	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4595634	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4764247	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764248	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764249	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4764251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5012088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6416262	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6416263	0.98[ASN][1000 genomes]
rs6488249	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488250	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488252	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488253	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6488254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6488256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6488257	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6488258	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488261	0.88[ASN][1000 genomes]
rs7313750	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7953886	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7956208	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7957278	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960611	0.96[ASN][1000 genomes]
rs7962246	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969125	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7970083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972187	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974909	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7976945	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7977902	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979762	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980801	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952545	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs952546	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10242800-10253800	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:10249600-10253400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:10250200-10253800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr12:10250600-10254200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:10251000-10254600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr12:10251200-10252600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:10251400-10255400	Enhancers	Placenta	Placenta
8	chr12:10251600-10253400	Weak transcription	Adipose Nuclei	Adipose
9	chr12:10251600-10253400	Weak transcription	Fetal Kidney	kidney
10	chr12:10251600-10253400	Weak transcription	Fetal Lung	lung
11	chr12:10251600-10253400	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:10251600-10253400	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:10251600-10253600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:10251600-10253600	Weak transcription	Left Ventricle	heart
15	chr12:10251600-10253600	Weak transcription	Lung	lung
16	chr12:10251600-10253800	Weak transcription	Fetal Thymus	thymus
17	chr12:10251600-10253800	Weak transcription	Ovary	ovary
18	chr12:10251800-10253400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:10251800-10253400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:10251800-10253400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:10251800-10253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:10251800-10253800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:10251800-10253800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:10251800-10253800	Weak transcription	Esophagus	oesophagus
25	chr12:10251800-10253800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:10252000-10253000	Weak transcription	Fetal Stomach	stomach
27	chr12:10252000-10253200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:10252000-10253400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:10252000-10253400	Enhancers	Colon Smooth Muscle	Colon
30	chr12:10252000-10253400	Weak transcription	Right Atrium	heart
31	chr12:10252000-10253400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:10252000-10253600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr12:10252000-10253600	Weak transcription	HUVEC	blood vessel
34	chr12:10252000-10253800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:10252400-10252600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:10252400-10252600	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:10252400-10252800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:10252400-10254000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:10252400-10255800	Enhancers	Primary monocytes fromperipheralblood	blood

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