Variant report

Variant	rs10878170
Chromosome Location	chr12:40552893-40552894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10437933	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10437934	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878160	0.83[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878161	0.89[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878162	0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878180	0.94[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10878199	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612806	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388591	0.81[YRI][hapmap]
rs1463721	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17442770	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248928	0.82[YRI][hapmap]
rs2249010	0.81[YRI][hapmap]
rs2249017	0.81[YRI][hapmap]
rs2307016	0.93[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638233	0.81[ASN][1000 genomes]
rs2708418	0.82[ASN][1000 genomes]
rs2708420	0.82[ASN][1000 genomes]
rs2708422	0.82[ASN][1000 genomes]
rs2708424	0.81[ASN][1000 genomes]
rs2708479	0.81[YRI][hapmap]
rs2708481	0.83[YRI][hapmap]
rs2723259	0.80[ASN][1000 genomes]
rs6581578	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307584	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs767940	0.82[CEU][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7969112	0.84[CEU][hapmap];0.88[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10878170	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 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	chr12:40550800-40553000	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr12:40551000-40553200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:40551200-40553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:40551200-40553200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:40551200-40553200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr12:40551200-40553600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr12:40551600-40553200	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:40551800-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:40551800-40553400	Enhancers	NHEK	skin
12	chr12:40552000-40553000	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:40552000-40556200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:40552200-40553000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr12:40552200-40553200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:40552200-40553200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:40552200-40553200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:40552200-40553200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:40552200-40553200	Flanking Active TSS	GM12878-XiMat	blood
20	chr12:40552200-40553400	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:40552400-40553000	Enhancers	Adipose Nuclei	Adipose
22	chr12:40552600-40553000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:40552600-40553000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr12:40552800-40553000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:40552800-40553000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:40552800-40553000	Enhancers	HMEC	breast

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