Variant report

Variant	rs4353978
Chromosome Location	chr5:59957073-59957074
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10805370	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10939857	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11739209	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745077	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11750609	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11951950	0.84[EUR][1000 genomes]
rs11956023	0.81[EUR][1000 genomes]
rs12655515	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1445852	0.84[EUR][1000 genomes]
rs1867702	0.81[EUR][1000 genomes]
rs2045356	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2591636	0.86[EUR][1000 genomes]
rs286153	0.86[EUR][1000 genomes]
rs286154	0.86[EUR][1000 genomes]
rs286155	0.86[EUR][1000 genomes]
rs34395679	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4538567	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4700379	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4700381	0.82[EUR][1000 genomes]
rs56137970	0.84[EUR][1000 genomes]
rs57521726	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62372964	0.82[EUR][1000 genomes]
rs6449483	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6449485	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6874072	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7719726	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs897672	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv968916	chr5:59944877-59962647	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4353978	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59926400-59967800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
5	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
6	chr5:59942800-59961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:59943400-59977000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:59945000-59961800	Weak transcription	HepG2	liver
9	chr5:59953200-59962000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:59953800-59958600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:59954000-59961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:59954000-59980200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:59954600-59969200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:59954800-59961800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr5:59955000-59961400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:59955000-59961400	Weak transcription	Dnd41	blood
17	chr5:59955000-59966600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:59955400-59959400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:59955400-59960000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:59955400-59961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:59955600-59965800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:59955800-59960800	Weak transcription	Placenta	Placenta
23	chr5:59956600-59957200	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:59956600-59957800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr5:59956800-59957200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:59956800-59961000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:59956800-59981800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr5:59957000-59957400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:59957000-59977000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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