Variant report

Variant	rs1388590
Chromosome Location	chr12:40547709-40547710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40545640-40549031..12:40691796-40694737	GM12878	blood:
2	chr12:40158520..40159448-chr12:40546284..40547792,5	MCF-7	breast:
3	12:40545640-40549031..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1031996	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784370	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10784381	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784386	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784387	0.83[ASN][1000 genomes]
rs10784428	0.80[ASN][1000 genomes]
rs10878113	0.86[ASN][1000 genomes]
rs10878220	0.82[ASN][1000 genomes]
rs10878222	0.81[ASN][1000 genomes]
rs1117378	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11175275	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11175326	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175327	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230710	0.81[ASN][1000 genomes]
rs12827541	0.82[ASN][1000 genomes]
rs1352876	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1388587	0.90[ASN][1000 genomes]
rs1388588	0.90[ASN][1000 genomes]
rs1388589	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1388591	0.94[ASN][1000 genomes]
rs1463719	0.99[ASN][1000 genomes]
rs1463720	0.99[ASN][1000 genomes]
rs1472118	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1482284	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1482285	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1482287	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482288	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1491927	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491928	0.90[ASN][1000 genomes]
rs1491929	0.96[ASN][1000 genomes]
rs1491930	0.94[ASN][1000 genomes]
rs1491931	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844921	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1844922	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1873611	0.91[ASN][1000 genomes]
rs1873612	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873613	0.91[ASN][1000 genomes]
rs1905121	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1948380	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2131082	0.96[ASN][1000 genomes]
rs2131083	0.96[ASN][1000 genomes]
rs2170503	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2201143	0.96[ASN][1000 genomes]
rs2220677	0.96[ASN][1000 genomes]
rs2248928	0.90[ASN][1000 genomes]
rs2249010	0.90[ASN][1000 genomes]
rs2249017	0.90[ASN][1000 genomes]
rs2404573	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638231	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2638232	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2638245	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638249	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638251	0.94[ASN][1000 genomes]
rs2638252	0.90[ASN][1000 genomes]
rs2638253	0.90[ASN][1000 genomes]
rs2638254	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638257	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638258	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638259	0.98[ASN][1000 genomes]
rs2638260	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638262	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638263	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638264	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638266	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638267	0.94[ASN][1000 genomes]
rs2708449	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2708464	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708466	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708467	0.96[ASN][1000 genomes]
rs2708470	0.96[ASN][1000 genomes]
rs2708472	0.96[ASN][1000 genomes]
rs2708473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708474	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708476	0.94[ASN][1000 genomes]
rs2708477	0.90[ASN][1000 genomes]
rs2708479	0.90[ASN][1000 genomes]
rs2708480	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708481	0.90[ASN][1000 genomes]
rs2708482	0.90[ASN][1000 genomes]
rs2708485	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708487	0.90[ASN][1000 genomes]
rs2708488	0.94[ASN][1000 genomes]
rs2708489	0.90[ASN][1000 genomes]
rs2708491	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708492	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708493	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708494	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812791	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4363681	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767967	0.84[ASN][1000 genomes]
rs4768221	0.84[ASN][1000 genomes]
rs6581514	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581519	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7132203	0.83[EUR][1000 genomes]
rs71443907	0.83[AMR][1000 genomes]
rs716231	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs722817	0.94[ASN][1000 genomes]
rs728622	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728623	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs728624	0.90[ASN][1000 genomes]
rs729216	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7306140	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7310430	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs900253	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937109	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937110	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937111	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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
rs1388590	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL
rs1388590	AC079630.2	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40546600-40547800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:40546600-40547800	Enhancers	A549	lung
3	chr12:40546600-40548400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:40546800-40548400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:40547000-40547800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:40547000-40547800	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:40547000-40548000	Enhancers	Primary B cells from cord blood	blood
8	chr12:40547200-40547800	Enhancers	HMEC	breast
9	chr12:40547200-40548000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr12:40547200-40558600	Weak transcription	Liver	Liver
11	chr12:40547400-40547800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:40547400-40547800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr12:40547400-40547800	Enhancers	GM12878-XiMat	blood
14	chr12:40547400-40548400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:40547400-40548600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:40547600-40551800	Weak transcription	NHEK	skin

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