Variant report

Variant	rs12220560
Chromosome Location	chr10:43706976-43706977
allele	C/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	EGR1	chr10:43706448-43707096	HCT-116	colon:	n/a	chr10:43706621-43706632 chr10:43706621-43706631 chr10:43706621-43706631 chr10:43706621-43706632 chr10:43706619-43706633
2	EGR1	chr10:43706332-43706999	HCT-116	colon:	n/a	chr10:43706621-43706632 chr10:43706621-43706631 chr10:43706621-43706631 chr10:43706621-43706632 chr10:43706619-43706633

No.	Distal block	Cell Line	Cell type
1	chr10:43705914..43707657-chr10:43711294..43713443,2	MCF-7	breast:
2	chr10:43705829..43707653-chr10:43720065..43721565,2	K562	blood:
3	chr10:43705495..43708277-chr10:43710722..43714581,3	K562	blood:

Variant related genes	Relation type
RASGEF1A	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1059484	0.90[EUR][1000 genomes]
rs10793422	0.94[EUR][1000 genomes]
rs10793424	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10793426	0.93[EUR][1000 genomes]
rs10793427	0.91[EUR][1000 genomes]
rs10899778	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10899779	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10899780	0.93[EUR][1000 genomes]
rs10899781	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10899782	0.95[EUR][1000 genomes]
rs10899786	0.93[EUR][1000 genomes]
rs10899787	0.90[EUR][1000 genomes]
rs11238476	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11238479	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11238481	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11238483	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11238485	0.95[EUR][1000 genomes]
rs11238490	0.91[EUR][1000 genomes]
rs11528481	0.95[EUR][1000 genomes]
rs12220534	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12268309	0.97[EUR][1000 genomes]
rs12356643	0.86[EUR][1000 genomes]
rs12360493	0.89[EUR][1000 genomes]
rs12416428	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1254958	0.91[EUR][1000 genomes]
rs1254959	0.92[EUR][1000 genomes]
rs1254960	0.94[EUR][1000 genomes]
rs1254962	0.93[EUR][1000 genomes]
rs1254963	0.93[EUR][1000 genomes]
rs1254965	0.91[EUR][1000 genomes]
rs1254967	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1254968	0.91[EUR][1000 genomes]
rs1270015	0.85[EUR][1000 genomes]
rs1317214	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1864400	0.82[EUR][1000 genomes]
rs1879310	0.95[EUR][1000 genomes]
rs1915142	0.92[EUR][1000 genomes]
rs2003317	0.90[EUR][1000 genomes]
rs2075912	0.87[EUR][1000 genomes]
rs2115817	0.90[EUR][1000 genomes]
rs2249005	0.87[EUR][1000 genomes]
rs2257767	0.88[EUR][1000 genomes]
rs2293020	0.91[EUR][1000 genomes]
rs2435337	0.90[EUR][1000 genomes]
rs2435338	0.89[EUR][1000 genomes]
rs2435339	0.89[EUR][1000 genomes]
rs2435354	0.89[EUR][1000 genomes]
rs2435376	0.87[EUR][1000 genomes]
rs2435377	0.88[EUR][1000 genomes]
rs2435383	0.90[EUR][1000 genomes]
rs2503848	0.90[EUR][1000 genomes]
rs2503853	0.89[EUR][1000 genomes]
rs2503860	0.90[EUR][1000 genomes]
rs2503863	0.90[EUR][1000 genomes]
rs2503864	0.90[EUR][1000 genomes]
rs2503881	0.90[EUR][1000 genomes]
rs2505506	0.89[EUR][1000 genomes]
rs2505514	0.87[EUR][1000 genomes]
rs2505553	0.90[EUR][1000 genomes]
rs2505557	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2565200	0.87[EUR][1000 genomes]
rs2565201	0.87[EUR][1000 genomes]
rs2742237	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2742239	0.87[EUR][1000 genomes]
rs2742240	0.81[EUR][1000 genomes]
rs2742241	0.82[EUR][1000 genomes]
rs4648313	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60845448	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61268333	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61845684	0.93[EUR][1000 genomes]
rs7073849	0.93[EUR][1000 genomes]
rs7093409	0.93[EUR][1000 genomes]
rs7096500	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7098236	0.93[EUR][1000 genomes]
rs7098237	0.93[EUR][1000 genomes]
rs715106	0.83[EUR][1000 genomes]
rs741968	0.87[EUR][1000 genomes]
rs871763	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12220560	CSGALNACT2	cis	Artery Tibial	GTEx
rs12220560	CSGALNACT2	cis	Heart Left Ventricle	GTEx
rs12220560	CSGALNACT2	cis	lung	GTEx
rs12220560	CSGALNACT2	cis	Thyroid	GTEx
rs12220560	CSGALNACT2	cis	Nerve Tibial	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43698000-43722800	Weak transcription	Gastric	stomach
2	chr10:43698200-43707400	Weak transcription	Brain Substantia Nigra	brain
3	chr10:43698400-43710800	Weak transcription	Esophagus	oesophagus
4	chr10:43699400-43716800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr10:43699400-43724600	Weak transcription	Right Atrium	heart
6	chr10:43701200-43707200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:43705800-43708000	Enhancers	Fetal Brain Female	brain
8	chr10:43705800-43708400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr10:43706000-43707000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:43706000-43707200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:43706000-43708200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:43706200-43707000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr10:43706200-43707200	Enhancers	Primary T cells fromperipheralblood	blood
14	chr10:43706200-43707600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:43706200-43707600	Enhancers	Brain Angular Gyrus	brain
16	chr10:43706200-43707800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr10:43706200-43708000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:43706200-43708200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:43706200-43708200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr10:43706200-43708200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr10:43706200-43708200	Enhancers	HMEC	breast
22	chr10:43706400-43707000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr10:43706400-43707400	Weak transcription	Fetal Brain Male	brain
24	chr10:43706400-43708000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr10:43706400-43708200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr10:43706600-43707000	Weak transcription	Brain Anterior Caudate	brain
27	chr10:43706600-43708600	Enhancers	Brain Hippocampus Middle	brain
28	chr10:43706800-43707600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:43706800-43707600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:43706800-43708600	Enhancers	Fetal Heart	heart
31	chr10:43706800-43709800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr10:43706800-43711600	Weak transcription	Spleen	Spleen

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