Variant report

Variant	rs56191602
Chromosome Location	chr5:59954444-59954445
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10939855	0.86[ASN][1000 genomes]
rs10939856	0.87[ASN][1000 genomes]
rs10939857	0.80[EUR][1000 genomes]
rs10939860	0.85[EUR][1000 genomes]
rs10939862	0.86[EUR][1000 genomes]
rs11739209	0.80[EUR][1000 genomes]
rs11739724	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740327	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11741754	0.80[ASN][1000 genomes]
rs11745077	0.81[EUR][1000 genomes]
rs11745627	0.93[EUR][1000 genomes]
rs11948543	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951503	0.96[ASN][1000 genomes]
rs11951950	0.87[ASN][1000 genomes]
rs11952735	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11955398	0.80[ASN][1000 genomes]
rs11956023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11959922	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12186391	0.85[EUR][1000 genomes]
rs12514253	0.86[EUR][1000 genomes]
rs12515025	0.85[EUR][1000 genomes]
rs12517174	0.82[ASN][1000 genomes]
rs12522801	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1379114	0.86[EUR][1000 genomes]
rs1379115	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1379116	0.99[ASN][1000 genomes]
rs1379117	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562235	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17387940	0.83[ASN][1000 genomes]
rs1816899	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1824120	0.85[EUR][1000 genomes]
rs1870014	0.85[EUR][1000 genomes]
rs2061250	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2198865	1.00[ASN][1000 genomes]
rs2409792	0.86[EUR][1000 genomes]
rs248911	0.84[EUR][1000 genomes]
rs249070	0.87[ASN][1000 genomes]
rs2591636	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs286153	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286154	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs286155	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs286156	0.90[ASN][1000 genomes]
rs286158	0.90[ASN][1000 genomes]
rs2898287	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34395679	0.81[EUR][1000 genomes]
rs3857236	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3958943	0.88[ASN][1000 genomes]
rs4538567	0.89[EUR][1000 genomes]
rs4700378	0.81[ASN][1000 genomes]
rs4700379	0.83[ASN][1000 genomes]
rs4700380	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4700381	0.88[ASN][1000 genomes]
rs5012862	0.82[ASN][1000 genomes]
rs55720622	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55768631	0.88[ASN][1000 genomes]
rs56137970	0.85[ASN][1000 genomes]
rs56166952	0.94[ASN][1000 genomes]
rs56726435	0.80[ASN][1000 genomes]
rs59155887	0.99[ASN][1000 genomes]
rs62372964	0.87[ASN][1000 genomes]
rs62373024	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62373025	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6877561	0.90[ASN][1000 genomes]
rs6896942	0.80[ASN][1000 genomes]
rs755077	0.86[EUR][1000 genomes]
rs7707698	0.85[EUR][1000 genomes]
rs7736518	0.84[EUR][1000 genomes]
rs9686489	0.85[EUR][1000 genomes]
rs9942410	0.87[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
rs56191602	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 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	chr5:59929400-59954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:59933400-59965200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:59933600-59981000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:59936600-59961400	Weak transcription	Thymus	Thymus
6	chr5:59936800-59961800	Weak transcription	Fetal Thymus	thymus
7	chr5:59942800-59961600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:59943400-59977000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:59945000-59961800	Weak transcription	HepG2	liver
10	chr5:59952800-59955000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:59953000-59954600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:59953200-59955000	Weak transcription	Placenta	Placenta
13	chr5:59953200-59962000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:59953400-59955400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:59953800-59958600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:59954000-59955400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:59954000-59961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:59954000-59980200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:59954200-59955000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:59954400-59955400	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr5:59954400-59956600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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