Variant report

Variant	rs2638258
Chromosome Location	chr12:40552256-40552257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-1	chr12:40552238-40552325	XLOC_010052
2	lnc-SLC2A13-1	chr12:40552238-40552325	XLOC_010052

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1031996	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10748014	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10784370	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs10784381	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784386	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784387	0.80[ASN][1000 genomes]
rs10784428	0.83[ASN][1000 genomes]
rs10878113	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10878220	0.85[ASN][1000 genomes]
rs10878222	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs10878224	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs1117378	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11175275	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11175326	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175327	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175656	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs12827541	0.85[ASN][1000 genomes]
rs1352876	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1388587	0.93[ASN][1000 genomes]
rs1388588	0.93[ASN][1000 genomes]
rs1388589	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1388590	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388591	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1463719	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1463720	0.96[ASN][1000 genomes]
rs1472118	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1482284	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1482285	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1482287	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1482288	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491927	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1491928	0.93[ASN][1000 genomes]
rs1491929	0.99[ASN][1000 genomes]
rs1491930	0.91[ASN][1000 genomes]
rs1491931	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1602578	0.83[ASN][1000 genomes]
rs1844921	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1844922	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873611	0.94[ASN][1000 genomes]
rs1873612	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873613	0.94[ASN][1000 genomes]
rs1905121	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1948380	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131082	0.99[ASN][1000 genomes]
rs2131083	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2170503	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2201143	0.99[ASN][1000 genomes]
rs2220677	0.99[ASN][1000 genomes]
rs2248928	0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2249010	0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2249017	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2404573	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2638231	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638232	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2638245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638249	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638251	0.98[ASN][1000 genomes]
rs2638252	0.93[ASN][1000 genomes]
rs2638253	0.93[ASN][1000 genomes]
rs2638254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638257	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638259	0.97[ASN][1000 genomes]
rs2638260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638262	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638263	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638264	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638266	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638267	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2708449	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708466	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708467	0.99[ASN][1000 genomes]
rs2708470	0.99[ASN][1000 genomes]
rs2708472	0.99[ASN][1000 genomes]
rs2708473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708474	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708476	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2708477	0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2708479	0.83[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2708480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708481	0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2708482	0.93[ASN][1000 genomes]
rs2708485	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708487	0.93[ASN][1000 genomes]
rs2708488	0.98[ASN][1000 genomes]
rs2708489	0.93[ASN][1000 genomes]
rs2708491	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708492	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708493	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708494	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812791	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4360759	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4363681	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767967	0.87[ASN][1000 genomes]
rs4768221	0.87[ASN][1000 genomes]
rs6581514	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581519	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7132203	0.84[EUR][1000 genomes]
rs716231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722817	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs728622	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs728623	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs728624	0.93[ASN][1000 genomes]
rs729216	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7306140	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7310430	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878010	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs900253	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937109	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937110	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937111	0.91[EUR][1000 genomes];0.83[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	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2638258	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL
rs2638258	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40547200-40558600	Weak transcription	Liver	Liver
2	chr12:40548800-40553800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:40550600-40552800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:40550800-40553000	Enhancers	Pancreatic Islets	Pancreatic Islet
5	chr12:40551000-40553200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:40551200-40552600	Enhancers	HMEC	breast
7	chr12:40551200-40553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:40551200-40553200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:40551200-40553200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:40551200-40553600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:40551600-40553200	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:40551800-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:40551800-40553400	Enhancers	NHEK	skin
14	chr12:40552000-40553000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr12:40552000-40556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:40552200-40553000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr12:40552200-40553200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:40552200-40553200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
19	chr12:40552200-40553200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:40552200-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:40552200-40553200	Flanking Active TSS	GM12878-XiMat	blood
22	chr12:40552200-40553400	Enhancers	Primary hematopoietic stem cells	blood

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