Variant report

Variant	rs937111
Chromosome Location	chr12:40503033-40503034
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40404217..40405558-chr12:40500388..40503110,15	MCF-7	breast:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

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

Chromatin state (count:7 , 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	chr12:40501600-40504200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:40501600-40504400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:40501600-40504400	Weak transcription	NHDF-Ad	bronchial
5	chr12:40502200-40503200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:40502600-40504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:40503000-40503200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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