Variant report

Variant	rs6752139
Chromosome Location	chr2:127969173-127969174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10167294	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10928764	0.85[EUR][1000 genomes]
rs1143407	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11899601	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613252	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613254	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12613413	0.89[EUR][1000 genomes]
rs12614320	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12617858	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12619391	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13017103	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13390029	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13403918	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13409933	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13414676	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13429925	0.89[EUR][1000 genomes]
rs2134794	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28807127	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34441363	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34487399	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34601617	0.89[EUR][1000 genomes]
rs34703177	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3738948	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3893313	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4150434	0.89[EUR][1000 genomes]
rs4150492	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4150506	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4150514	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4300780	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4359587	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4528711	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4662721	0.86[EUR][1000 genomes]
rs58063879	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59027829	0.83[EUR][1000 genomes]
rs6430937	0.89[EUR][1000 genomes]
rs6716392	0.83[EUR][1000 genomes]
rs6738811	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6747862	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9752366	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9923	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS 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
9	nsv961678	chr2:127961305-127979990	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv3331416	chr2:127962771-127980988	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6752139	AC068282.3	cis	Esophagus Mucosa	GTEx
rs6752139	AC068282.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6752139	AC068282.3	cis	Esophagus Muscularis	GTEx
rs6752139	AC068282.3	cis	Muscle Skeletal	GTEx
rs6752139	AC068282.3	cis	Nerve Tibial	GTEx
rs6752139	AC068282.3	cis	Artery Aorta	GTEx
rs6752139	AC068282.3	cis	Adipose Subcutaneous	GTEx
rs6752139	AC068282.3	cis	Whole Blood	GTEx
rs6752139	AC068282.3	cis	Stomach	GTEx
rs6752139	AC068282.3	cis	Thyroid	GTEx
rs6752139	AC068282.3	cis	Heart Left Ventricle	GTEx
rs6752139	AC068282.3	cis	lung	GTEx
rs6752139	AC068282.3	cis	Artery Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127948800-127973400	Weak transcription	HMEC	breast
2	chr2:127952200-127975200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:127956400-127975800	Weak transcription	Fetal Kidney	kidney
4	chr2:127966800-127975400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:127967200-127975400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:127967400-127973200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:127967400-127973200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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