Variant report

Variant	rs10784387
Chromosome Location	chr12:40535118-40535119
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-1	chr12:40534259-40536436	XLOC_010052
2	lnc-SLC2A13-1	chr12:40534728-40536678	ENSG00000260943.1

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1031996	0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs10784381	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs10784386	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10878113	0.92[ASN][1000 genomes]
rs11175275	0.90[ASN][1000 genomes]
rs11175326	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11175327	0.84[ASN][1000 genomes]
rs12230710	0.85[ASN][1000 genomes]
rs1352876	0.85[JPT][hapmap]
rs1388587	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1388588	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1388590	0.83[ASN][1000 genomes]
rs1388591	0.91[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1463719	0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1463720	0.84[ASN][1000 genomes]
rs1482284	0.83[ASN][1000 genomes]
rs1482285	0.92[ASN][1000 genomes]
rs1491928	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1491929	0.81[ASN][1000 genomes]
rs1491930	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491931	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1873611	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1873612	0.80[ASN][1000 genomes]
rs1873613	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2131082	0.81[ASN][1000 genomes]
rs2131083	0.81[ASN][1000 genomes]
rs2170503	0.85[JPT][hapmap]
rs2201143	0.81[ASN][1000 genomes]
rs2220677	0.81[ASN][1000 genomes]
rs2248928	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249010	0.87[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2249017	0.86[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404573	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2638252	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638253	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2638254	0.85[JPT][hapmap]
rs2638257	0.80[ASN][1000 genomes]
rs2638258	0.80[ASN][1000 genomes]
rs2638259	0.83[ASN][1000 genomes]
rs2638260	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2638262	0.83[ASN][1000 genomes]
rs2638263	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2638264	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2638266	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs2638267	0.91[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2708464	0.82[ASN][1000 genomes]
rs2708467	0.81[ASN][1000 genomes]
rs2708470	0.81[ASN][1000 genomes]
rs2708472	0.81[ASN][1000 genomes]
rs2708473	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2708474	0.80[ASN][1000 genomes]
rs2708477	0.87[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708479	0.87[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708480	0.85[JPT][hapmap]
rs2708481	0.86[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708482	0.87[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708487	0.87[CEU][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2708489	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4363681	0.80[ASN][1000 genomes]
rs7132203	0.83[ASN][1000 genomes]
rs716231	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs722817	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs728624	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs767940	0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs878010	0.83[JPT][hapmap]
rs900253	0.83[JPT][hapmap]
rs937109	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs937110	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10784387	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40532400-40535600	Weak transcription	HMEC	breast
2	chr12:40532600-40535600	Weak transcription	NHEK	skin
3	chr12:40532600-40535800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:40532800-40535800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:40532800-40543800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:40535000-40537200	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links