Variant report

Variant	rs2404573
Chromosome Location	chr12:40504495-40504496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr12:40504393-40504741	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr12:40504483-40504682	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40404668..40405271-chr12:40503732..40504617,2	MCF-7	breast:
2	chr12:40471822..40473887-chr12:40503085..40505946,2	K562	blood:

Variant related genes	Relation type
SLC2A13	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1031996	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10748014	0.84[JPT][hapmap]
rs10784370	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs10784381	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784386	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784387	0.87[ASN][1000 genomes]
rs10878113	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1117378	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11175275	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11175326	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11175327	0.83[ASN][1000 genomes]
rs11175656	0.84[JPT][hapmap]
rs12230710	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352876	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1388589	0.84[EUR][1000 genomes]
rs1388590	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1388591	0.89[JPT][hapmap]
rs1463719	0.85[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1463720	0.81[ASN][1000 genomes]
rs1472118	0.82[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1482284	0.95[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1482285	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1482287	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1482288	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491927	0.82[EUR][1000 genomes]
rs1491931	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1873612	0.84[EUR][1000 genomes]
rs1905121	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1948380	0.82[EUR][1000 genomes]
rs2170503	0.93[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2248928	0.89[JPT][hapmap]
rs2249010	0.89[JPT][hapmap]
rs2249017	0.89[JPT][hapmap]
rs2638231	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2638232	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638245	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs2638249	0.82[EUR][1000 genomes]
rs2638254	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2638257	0.84[EUR][1000 genomes]
rs2638258	0.84[EUR][1000 genomes]
rs2638259	0.81[ASN][1000 genomes]
rs2638260	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638262	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638263	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638264	0.93[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638266	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638267	0.89[JPT][hapmap]
rs2708449	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708464	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708466	0.84[EUR][1000 genomes]
rs2708473	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2708474	0.83[EUR][1000 genomes]
rs2708477	0.89[JPT][hapmap]
rs2708479	0.89[JPT][hapmap]
rs2708480	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2708481	0.89[JPT][hapmap]
rs2708485	0.82[EUR][1000 genomes]
rs2708491	0.80[EUR][1000 genomes]
rs2708492	0.80[EUR][1000 genomes]
rs2708494	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs3812791	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4360759	0.93[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap]
rs4363681	0.84[EUR][1000 genomes]
rs6581514	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581519	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7132203	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs716231	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs728622	0.82[EUR][1000 genomes]
rs728623	0.82[EUR][1000 genomes]
rs729216	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7306140	0.89[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7310430	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs878010	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs900253	0.92[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs937109	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937110	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937111	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2404573	AC079630.2	cis	Esophagus Mucosa	GTEx
rs2404573	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40501200-40510200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:40503200-40504800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:40504200-40504600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:40504200-40505000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:40504400-40504800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:40504400-40505200	Enhancers	NHDF-Ad	bronchial

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