Variant report

Variant	rs12827541
Chromosome Location	chr12:40609979-40609980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031996	0.85[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10748014	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784381	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10784386	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs10784428	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784444	0.84[JPT][hapmap]
rs10878220	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878222	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878224	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878245	0.83[JPT][hapmap]
rs10878249	0.83[JPT][hapmap]
rs11175326	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs11175327	0.81[ASN][1000 genomes]
rs11175656	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1352876	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs1388587	0.81[ASN][1000 genomes]
rs1388589	0.83[ASN][1000 genomes]
rs1388590	0.82[ASN][1000 genomes]
rs1463719	0.81[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs1463720	0.81[ASN][1000 genomes]
rs1472118	0.82[CHB][hapmap]
rs1491927	0.87[ASN][1000 genomes]
rs1491928	0.81[ASN][1000 genomes]
rs1491929	0.84[ASN][1000 genomes]
rs1491931	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs1491938	0.83[JPT][hapmap]
rs1602578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844921	0.88[ASN][1000 genomes]
rs1844922	0.88[ASN][1000 genomes]
rs1873611	0.80[ASN][1000 genomes]
rs1873612	0.85[ASN][1000 genomes]
rs1873613	0.80[ASN][1000 genomes]
rs1948380	0.87[ASN][1000 genomes]
rs2131082	0.84[ASN][1000 genomes]
rs2131083	0.84[ASN][1000 genomes]
rs2170503	0.84[JPT][hapmap]
rs2201143	0.84[ASN][1000 genomes]
rs2220677	0.84[ASN][1000 genomes]
rs2248928	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2249010	0.81[ASN][1000 genomes]
rs2249017	0.81[ASN][1000 genomes]
rs2638245	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2638249	0.87[ASN][1000 genomes]
rs2638251	0.86[ASN][1000 genomes]
rs2638252	0.81[ASN][1000 genomes]
rs2638253	0.81[ASN][1000 genomes]
rs2638254	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2638257	0.85[ASN][1000 genomes]
rs2638258	0.85[ASN][1000 genomes]
rs2638259	0.82[ASN][1000 genomes]
rs2638260	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2638262	0.82[ASN][1000 genomes]
rs2638263	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2638264	0.82[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2638266	0.86[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708464	0.84[ASN][1000 genomes]
rs2708466	0.84[ASN][1000 genomes]
rs2708467	0.84[ASN][1000 genomes]
rs2708470	0.84[ASN][1000 genomes]
rs2708472	0.84[ASN][1000 genomes]
rs2708473	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs2708474	0.85[ASN][1000 genomes]
rs2708476	0.86[ASN][1000 genomes]
rs2708477	0.81[ASN][1000 genomes]
rs2708479	0.81[ASN][1000 genomes]
rs2708480	0.86[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2708481	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2708482	0.81[ASN][1000 genomes]
rs2708485	0.87[ASN][1000 genomes]
rs2708487	0.81[ASN][1000 genomes]
rs2708488	0.86[ASN][1000 genomes]
rs2708489	0.81[ASN][1000 genomes]
rs2708491	0.87[ASN][1000 genomes]
rs2708492	0.87[ASN][1000 genomes]
rs2708493	0.87[ASN][1000 genomes]
rs2708494	0.80[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4360759	0.82[CHB][hapmap]
rs4363681	0.85[ASN][1000 genomes]
rs4767967	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768221	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716231	0.86[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs728622	0.87[ASN][1000 genomes]
rs728623	0.87[ASN][1000 genomes]
rs728624	0.81[ASN][1000 genomes]
rs7306140	0.82[CHB][hapmap]
rs7955902	0.83[JPT][hapmap]
rs878010	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs900253	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs937109	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs937110	0.81[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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs12827541	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL
rs12827541	AC079630.2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40604200-40611000	Weak transcription	Fetal Kidney	kidney
2	chr12:40605200-40610400	Weak transcription	A549	lung
3	chr12:40608800-40611400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:40609200-40610000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:40609200-40611200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:40609400-40610000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:40609400-40610800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:40609400-40611000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:40609400-40611000	Enhancers	Hela-S3	cervix
10	chr12:40609400-40611000	Enhancers	HMEC	breast
11	chr12:40609600-40610000	Enhancers	Primary B cells from cord blood	blood
12	chr12:40609600-40610000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:40609600-40610400	Enhancers	NHEK	skin
14	chr12:40609600-40610600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:40609600-40611000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr12:40609800-40610200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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