Variant report

Variant	rs29001228
Chromosome Location	chr4:100047084-100047085
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99914784..99916943-chr4:100045840..100048250,2	K562	blood:

Variant related genes	Relation type
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 100 )
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]
rs17028770	0.83[AMR][1000 genomes]
rs2018417	0.83[AMR][1000 genomes]
rs28364314	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28720156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][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]
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	0.86[EUR][1000 genomes]
rs58168287	0.86[EUR][1000 genomes]
rs59626468	0.86[EUR][1000 genomes]
rs62323214	1.00[AFR][1000 genomes]
rs62323217	1.00[AFR][1000 genomes]
rs62323230	0.83[AMR][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	0.86[EUR][1000 genomes]
rs6827292	0.83[AMR][1000 genomes]
rs7692198	0.86[EUR][1000 genomes]
rs7699232	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv3528915	chr4:100025155-100096234	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv3528916	chr4:100025155-100096234	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs29001228	ADH5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100012800-100063800	Weak transcription	Aorta	Aorta
2	chr4:100023000-100055600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:100035000-100098200	Weak transcription	Ovary	ovary
4	chr4:100038800-100055200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:100039800-100064800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:100040000-100050800	Weak transcription	Fetal Intestine Large	intestine
7	chr4:100044000-100056600	Weak transcription	Fetal Lung	lung
8	chr4:100044400-100063600	Weak transcription	Fetal Intestine Small	intestine
9	chr4:100045000-100048800	Strong transcription	Liver	Liver
10	chr4:100046000-100048000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:100046200-100048800	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr4:100046400-100048600	Strong transcription	HepG2	liver
13	chr4:100046600-100048000	Strong transcription	Duodenum Mucosa	Duodenum

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