Variant report

Variant	rs2708489
Chromosome Location	chr12:40562442-40562443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1031996	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10748014	0.84[JPT][hapmap]
rs10784381	0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10784386	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784387	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10878220	0.81[ASN][1000 genomes]
rs10878222	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1117378	0.81[ASN][1000 genomes]
rs11175326	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs11175327	0.89[ASN][1000 genomes]
rs11175656	0.84[JPT][hapmap]
rs12827541	0.81[ASN][1000 genomes]
rs1352876	0.81[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1388587	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1388588	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1388589	0.91[ASN][1000 genomes]
rs1388590	0.90[ASN][1000 genomes]
rs1388591	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1463719	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs1463720	0.91[ASN][1000 genomes]
rs1472118	0.89[JPT][hapmap]
rs1482284	0.87[ASN][1000 genomes]
rs1482287	0.82[ASN][1000 genomes]
rs1482288	0.81[ASN][1000 genomes]
rs1491927	0.94[ASN][1000 genomes]
rs1491928	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491929	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1491930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491931	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1844921	0.93[ASN][1000 genomes]
rs1844922	0.93[ASN][1000 genomes]
rs1873611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873612	0.93[ASN][1000 genomes]
rs1873613	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1905121	0.82[ASN][1000 genomes]
rs1948380	0.94[ASN][1000 genomes]
rs2131082	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2131083	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2170503	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2201143	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2220677	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2248928	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2404573	0.89[JPT][hapmap]
rs2638231	0.81[ASN][1000 genomes]
rs2638232	0.81[ASN][1000 genomes]
rs2638245	0.81[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs2638249	0.94[ASN][1000 genomes]
rs2638251	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2638252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638254	0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2638257	0.93[ASN][1000 genomes]
rs2638258	0.93[ASN][1000 genomes]
rs2638259	0.90[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2638260	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638262	0.90[ASN][1000 genomes]
rs2638263	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638264	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638266	0.81[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638267	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708449	0.82[ASN][1000 genomes]
rs2708464	0.91[ASN][1000 genomes]
rs2708466	0.91[ASN][1000 genomes]
rs2708467	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2708470	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2708472	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2708473	0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs2708474	0.93[ASN][1000 genomes]
rs2708476	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2708477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708479	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708480	0.81[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2708481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708482	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708485	0.94[ASN][1000 genomes]
rs2708487	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708488	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2708491	0.94[ASN][1000 genomes]
rs2708492	0.94[ASN][1000 genomes]
rs2708493	0.94[ASN][1000 genomes]
rs2708494	0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4360759	0.89[JPT][hapmap]
rs4363681	0.93[ASN][1000 genomes]
rs4767967	0.83[ASN][1000 genomes]
rs4768221	0.83[ASN][1000 genomes]
rs6581514	0.82[ASN][1000 genomes]
rs6581519	0.82[ASN][1000 genomes]
rs716231	0.81[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs722817	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728622	0.94[ASN][1000 genomes]
rs728623	0.94[ASN][1000 genomes]
rs728624	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729216	0.82[ASN][1000 genomes]
rs7306140	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7310430	0.82[ASN][1000 genomes]
rs878010	0.89[JPT][hapmap]
rs900253	0.89[JPT][hapmap]
rs937109	0.81[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs937110	0.88[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	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
5	esv3398206	chr12:40556364-40581392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2708489	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40557400-40564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40561800-40563200	Enhancers	Primary B cells from cord blood	blood
3	chr12:40562000-40562600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:40562000-40563000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr12:40562000-40563000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr12:40562000-40563200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:40562200-40562600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr12:40562200-40562600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:40562200-40562800	Enhancers	Primary B cells from peripheral blood	blood
10	chr12:40562200-40563000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:40562400-40562600	Enhancers	GM12878-XiMat	blood
12	chr12:40562400-40562800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr12:40562400-40563000	Enhancers	Primary T cells from cord blood	blood

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