Variant report

Variant	rs27653
Chromosome Location	chr5:59794230-59794231
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs26955	0.99[ASN][1000 genomes]
rs26956	0.89[ASN][1000 genomes]
rs27221	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35381	0.93[ASN][1000 genomes]
rs35386	0.99[ASN][1000 genomes]
rs35387	0.99[ASN][1000 genomes]
rs3857232	0.82[AFR][1000 genomes]
rs42448	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs457053	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs27653	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59782000-59801000	Weak transcription	Fetal Brain Male	brain
2	chr5:59789600-59795400	Weak transcription	Aorta	Aorta
3	chr5:59790000-59795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:59790400-59794800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:59791000-59794800	Enhancers	Brain Cingulate Gyrus	brain
6	chr5:59791000-59795200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:59791200-59795000	Enhancers	HMEC	breast
8	chr5:59791400-59794600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:59791400-59801000	Weak transcription	Primary B cells from cord blood	blood
10	chr5:59792200-59794800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr5:59792200-59795200	Enhancers	HepG2	liver
12	chr5:59792600-59798200	Weak transcription	GM12878-XiMat	blood
13	chr5:59792800-59794800	Enhancers	Brain Angular Gyrus	brain
14	chr5:59793000-59794800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr5:59793200-59794800	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr5:59793400-59794400	Enhancers	Fetal Stomach	stomach
17	chr5:59793400-59794400	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:59793600-59794400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:59793600-59794600	Enhancers	Colon Smooth Muscle	Colon
20	chr5:59793600-59794800	Enhancers	Osteobl	bone
21	chr5:59793600-59795200	Enhancers	Brain Hippocampus Middle	brain
22	chr5:59793800-59794400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:59793800-59794400	Enhancers	Brain Anterior Caudate	brain
24	chr5:59793800-59794600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:59793800-59795200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:59794000-59794400	Enhancers	NHEK	skin
27	chr5:59794200-59794400	Enhancers	Gastric	stomach
28	chr5:59794200-59794400	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr5:59794200-59794800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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