Variant report

Variant	rs57028254
Chromosome Location	chr4:100111947-100111948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs17028758	0.87[EUR][1000 genomes]
rs17028770	0.87[EUR][1000 genomes]
rs2213038	0.95[AFR][1000 genomes]
rs28720156	1.00[EUR][1000 genomes]
rs29001228	0.86[EUR][1000 genomes]
rs57351530	0.87[EUR][1000 genomes]
rs58168287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59626468	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6815396	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7692198	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924195	0.87[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	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1002574	chr4:100023999-100133693	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3355763	chr4:100070566-100376814	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv879657	chr4:100082154-100139366	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1014237	chr4:100102701-100365700	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1010988	chr4:100105463-100444445	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57028254	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100098600-100113400	Weak transcription	Aorta	Aorta
2	chr4:100098600-100113400	Weak transcription	Ovary	ovary
3	chr4:100099000-100112800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:100102200-100123400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:100107000-100114400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:100108400-100141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:100111400-100112000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:100111400-100112000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:100111400-100112000	Enhancers	Fetal Lung	lung
10	chr4:100111400-100112400	Enhancers	Liver	Liver
11	chr4:100111800-100112000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:100111800-100112000	Enhancers	Adipose Nuclei	Adipose

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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