Variant report

Variant	rs2638267
Chromosome Location	chr12:40543733-40543734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40543659..40545848-chr12:40705219..40707677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1031996	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10748014	0.84[JPT][hapmap]
rs10784381	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10784386	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10784387	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10878113	0.81[ASN][1000 genomes]
rs1117378	0.86[ASN][1000 genomes]
rs11175326	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11175327	0.92[ASN][1000 genomes]
rs11175656	0.84[JPT][hapmap]
rs1352876	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1388587	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388588	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1388589	0.89[ASN][1000 genomes]
rs1388590	0.94[ASN][1000 genomes]
rs1388591	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463719	0.82[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1463720	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1472118	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1482284	0.91[ASN][1000 genomes]
rs1482285	0.81[ASN][1000 genomes]
rs1482287	0.87[ASN][1000 genomes]
rs1482288	0.85[ASN][1000 genomes]
rs1491927	0.90[ASN][1000 genomes]
rs1491928	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491929	0.92[ASN][1000 genomes]
rs1491930	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1491931	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1844921	0.88[ASN][1000 genomes]
rs1844922	0.88[ASN][1000 genomes]
rs1873611	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1873612	0.91[ASN][1000 genomes]
rs1873613	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1905121	0.87[ASN][1000 genomes]
rs1948380	0.90[ASN][1000 genomes]
rs2131082	0.92[ASN][1000 genomes]
rs2131083	0.92[ASN][1000 genomes]
rs2170503	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2201143	0.92[ASN][1000 genomes]
rs2220677	0.92[ASN][1000 genomes]
rs2248928	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2249010	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]
rs2249017	0.96[CEU][hapmap];0.91[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]
rs2404573	0.89[JPT][hapmap]
rs2638231	0.85[ASN][1000 genomes]
rs2638232	0.86[ASN][1000 genomes]
rs2638245	0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2638249	0.90[ASN][1000 genomes]
rs2638251	0.91[ASN][1000 genomes]
rs2638252	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638253	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638254	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2638257	0.91[ASN][1000 genomes]
rs2638258	0.91[ASN][1000 genomes]
rs2638259	0.94[ASN][1000 genomes]
rs2638260	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2638262	0.94[ASN][1000 genomes]
rs2638263	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2638264	0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2638266	0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs2708449	0.87[ASN][1000 genomes]
rs2708464	0.93[ASN][1000 genomes]
rs2708466	0.90[ASN][1000 genomes]
rs2708467	0.92[ASN][1000 genomes]
rs2708470	0.92[ASN][1000 genomes]
rs2708472	0.92[ASN][1000 genomes]
rs2708473	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2708474	0.91[ASN][1000 genomes]
rs2708476	0.91[ASN][1000 genomes]
rs2708477	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708479	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]
rs2708480	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2708481	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708482	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708485	0.90[ASN][1000 genomes]
rs2708487	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708488	0.91[ASN][1000 genomes]
rs2708489	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2708491	0.90[ASN][1000 genomes]
rs2708492	0.90[ASN][1000 genomes]
rs2708493	0.89[ASN][1000 genomes]
rs2708494	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3812791	0.82[ASN][1000 genomes]
rs4360759	0.89[JPT][hapmap]
rs4363681	0.91[ASN][1000 genomes]
rs6581514	0.87[ASN][1000 genomes]
rs6581519	0.87[ASN][1000 genomes]
rs71443907	0.81[ASN][1000 genomes]
rs716231	0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs722817	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728622	0.90[ASN][1000 genomes]
rs728623	0.90[ASN][1000 genomes]
rs728624	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs729216	0.87[ASN][1000 genomes]
rs7306140	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7310430	0.87[ASN][1000 genomes]
rs878010	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs900253	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs937109	0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs937110	0.93[ASN][1000 genomes]
rs937111	0.81[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
rs2638267	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40532800-40543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:40541400-40546600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:40541800-40546600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:40543400-40544000	Enhancers	Adipose Nuclei	Adipose
5	chr12:40543400-40544200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:40543600-40543800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr12:40543600-40544000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:40543600-40544000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:40543600-40544000	Enhancers	Hela-S3	cervix

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