Variant report

Variant	rs28720156
Chromosome Location	chr4:100128536-100128537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10002449	0.83[AMR][1000 genomes]
rs10084896	0.83[AMR][1000 genomes]
rs17028370	1.00[AMR][1000 genomes]
rs17028758	0.87[EUR][1000 genomes]
rs17028770	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2018417	0.83[AMR][1000 genomes]
rs28364314	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28730601	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28730611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730641	0.83[AMR][1000 genomes]
rs28730643	0.83[AMR][1000 genomes]
rs28730644	0.83[AMR][1000 genomes]
rs28730645	0.83[AMR][1000 genomes]
rs28730646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28730649	0.83[AMR][1000 genomes]
rs28894371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28914786	0.83[AMR][1000 genomes]
rs29001228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs29001338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs29001342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55963727	0.83[AMR][1000 genomes]
rs57028254	1.00[EUR][1000 genomes]
rs57351530	0.87[EUR][1000 genomes]
rs58168287	1.00[EUR][1000 genomes]
rs59626468	1.00[EUR][1000 genomes]
rs62323231	0.83[AMR][1000 genomes]
rs62323233	0.83[AMR][1000 genomes]
rs62323234	1.00[AMR][1000 genomes]
rs62323235	1.00[AMR][1000 genomes]
rs62323236	0.83[AMR][1000 genomes]
rs62323237	0.83[AMR][1000 genomes]
rs62323238	0.83[AMR][1000 genomes]
rs62323240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62323241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62323242	1.00[AMR][1000 genomes]
rs62323244	0.83[AMR][1000 genomes]
rs62323245	1.00[AMR][1000 genomes]
rs62323246	1.00[AMR][1000 genomes]
rs62323247	1.00[AMR][1000 genomes]
rs62323248	0.83[AMR][1000 genomes]
rs62323249	0.83[AMR][1000 genomes]
rs62323250	1.00[AMR][1000 genomes]
rs62323251	1.00[AMR][1000 genomes]
rs62323252	0.83[AMR][1000 genomes]
rs62323254	1.00[AMR][1000 genomes]
rs62323255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62323256	0.83[AMR][1000 genomes]
rs62323257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62323258	1.00[AMR][1000 genomes]
rs62323259	0.83[AMR][1000 genomes]
rs62325160	0.83[AMR][1000 genomes]
rs62325161	0.83[AMR][1000 genomes]
rs62325182	0.83[AMR][1000 genomes]
rs62325183	0.83[AMR][1000 genomes]
rs62325184	0.83[AMR][1000 genomes]
rs62325185	0.83[AMR][1000 genomes]
rs62325186	0.83[AMR][1000 genomes]
rs62325187	0.83[AMR][1000 genomes]
rs62325188	0.83[AMR][1000 genomes]
rs62325190	0.83[AMR][1000 genomes]
rs62325192	0.83[AMR][1000 genomes]
rs62325193	0.83[AMR][1000 genomes]
rs62325194	0.83[AMR][1000 genomes]
rs62325195	0.83[AMR][1000 genomes]
rs62325196	0.83[AMR][1000 genomes]
rs62325197	0.83[AMR][1000 genomes]
rs62325198	0.83[AMR][1000 genomes]
rs62325199	0.83[AMR][1000 genomes]
rs62325200	0.83[AMR][1000 genomes]
rs62325201	1.00[AMR][1000 genomes]
rs62325202	0.83[AMR][1000 genomes]
rs62325203	0.83[AMR][1000 genomes]
rs62325204	1.00[AMR][1000 genomes]
rs62325205	0.83[AMR][1000 genomes]
rs62325208	0.83[AMR][1000 genomes]
rs62325209	0.83[AMR][1000 genomes]
rs62325210	0.83[AMR][1000 genomes]
rs62325212	1.00[AMR][1000 genomes]
rs62325213	1.00[AMR][1000 genomes]
rs62325236	0.83[AMR][1000 genomes]
rs62325237	0.83[AMR][1000 genomes]
rs62325238	0.83[AMR][1000 genomes]
rs62325239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62325240	0.83[AMR][1000 genomes]
rs62325241	0.83[AMR][1000 genomes]
rs62325242	0.83[AMR][1000 genomes]
rs62325245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6815396	1.00[EUR][1000 genomes]
rs6827292	0.83[AMR][1000 genomes]
rs7692198	1.00[EUR][1000 genomes]
rs7699232	0.83[AMR][1000 genomes]
rs924195	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv879658	chr4:100123776-100131163	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28720156	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100108400-100141600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:100115200-100129800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:100124600-100128600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:100126000-100130200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr4:100126600-100128600	Enhancers	Liver	Liver
6	chr4:100126800-100128600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:100127000-100129600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:100127000-100129800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:100127000-100129800	Weak transcription	Aorta	Aorta
10	chr4:100127000-100129800	Weak transcription	NHLF	lung
11	chr4:100127000-100130600	Weak transcription	HSMMtube	muscle
12	chr4:100127000-100131000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:100127000-100131200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:100127000-100139000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:100127000-100139400	Weak transcription	Ovary	ovary
16	chr4:100127000-100140200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:100127000-100142600	Weak transcription	Small Intestine	intestine
18	chr4:100127200-100128800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:100127400-100129200	Weak transcription	Fetal Kidney	kidney
20	chr4:100127400-100131000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:100127400-100139000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:100127600-100128600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:100127600-100128600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:100127600-100128600	Weak transcription	Fetal Lung	lung
25	chr4:100127600-100129600	Weak transcription	HepG2	liver
26	chr4:100127600-100130000	Weak transcription	NHDF-Ad	bronchial
27	chr4:100127600-100130600	Weak transcription	Fetal Intestine Small	intestine
28	chr4:100127600-100138800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:100128000-100130000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:100128200-100128600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:100128200-100128800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr4:100128200-100128800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:100128200-100129000	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:100128200-100130000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr4:100128200-100130200	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr4:100128400-100128600	Weak transcription	Left Ventricle	heart
37	chr4:100128400-100131400	Enhancers	iPS-20b Cell Line	embryonic stem cell

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