Variant report

Variant	rs55963727
Chromosome Location	chr4:100240064-100240065
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1693453	1.00[AFR][1000 genomes]
rs17028758	0.85[AMR][1000 genomes]
rs17028770	1.00[AMR][1000 genomes]
rs2018417	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2051429	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28364314	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28720156	0.83[AMR][1000 genomes]
rs28914786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs29001228	0.83[AMR][1000 genomes]
rs29001338	0.83[AMR][1000 genomes]
rs29001342	0.83[AMR][1000 genomes]
rs3098808	1.00[AFR][1000 genomes]
rs3114047	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	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
3	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
4	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
5	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
6	nsv1000659	chr4:100117276-100444445	Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv999549	chr4:100121609-100351749	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3353320	chr4:100147870-100425701	Genic enhancers ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3394995	chr4:100147890-100425671	Enhancers Genic enhancers Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	esv3446139	chr4:100213459-100244162	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3387812	chr4:100232775-100261923	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1002809	chr4:100234048-100285508	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv3394945	chr4:100237238-100266245	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv3465817	chr4:100238736-100267823	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	esv3465818	chr4:100238736-100267823	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55963727	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100231000-100243000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:100231200-100242800	Weak transcription	Gastric	stomach
3	chr4:100233000-100244400	Weak transcription	NHDF-Ad	bronchial
4	chr4:100237000-100241800	Transcr. at gene 5' and 3'	Fetal Lung	lung
5	chr4:100237400-100240400	Weak transcription	Colonic Mucosa	Colon
6	chr4:100238400-100240600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:100238600-100240600	Transcr. at gene 5' and 3'	Liver	Liver
8	chr4:100238800-100243000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:100239200-100240400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:100239200-100240400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:100239200-100242600	Active TSS	Stomach Smooth Muscle	stomach
12	chr4:100239200-100243000	Active TSS	Right Atrium	heart
13	chr4:100239200-100245000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:100239200-100245200	Weak transcription	Left Ventricle	heart
15	chr4:100239400-100240200	Weak transcription	Aorta	Aorta
16	chr4:100239400-100241200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:100240000-100240200	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
18	chr4:100240000-100240200	Active TSS	Lung	lung
19	chr4:100240000-100240200	Flanking Active TSS	Rectal Smooth Muscle	rectum
20	chr4:100240000-100240600	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr4:100240000-100240800	Active TSS	Psoas Muscle	Psoas
22	chr4:100240000-100241800	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr4:100240000-100242400	ZNF genes & repeats	Fetal Brain Male	brain
24	chr4:100240000-100242800	Active TSS	Ovary	ovary
25	chr4:100240000-100243000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:100240000-100243200	Active TSS	Duodenum Smooth Muscle	Duodenum

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