Variant report

Variant	rs62373023
Chromosome Location	chr5:59911693-59911694
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10939855	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10939856	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11740327	0.90[ASN][1000 genomes]
rs11745627	0.89[ASN][1000 genomes]
rs11951503	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1379116	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1445852	0.81[ASN][1000 genomes]
rs153152	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1816899	0.90[ASN][1000 genomes]
rs206789	0.85[ASN][1000 genomes]
rs2198865	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs248912	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs249070	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs286148	0.87[ASN][1000 genomes]
rs286154	0.87[ASN][1000 genomes]
rs3958943	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4504343	0.93[EUR][1000 genomes]
rs4538566	0.93[EUR][1000 genomes]
rs55768631	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56166952	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56347749	0.93[EUR][1000 genomes]
rs59155887	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62373024	0.92[ASN][1000 genomes]
rs62373025	0.95[ASN][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	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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62373023	ERCC8	Cis_1M	lymphoblastoid	RTeQTL
rs62373023	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59887600-59925800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:59891200-59926200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:59892000-59912200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:59894400-59926600	Weak transcription	Thymus	Thymus
5	chr5:59894800-59933600	Weak transcription	Hela-S3	cervix
6	chr5:59899400-59912600	Weak transcription	Fetal Thymus	thymus
7	chr5:59899400-59928000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:59899800-59924800	Weak transcription	HepG2	liver
9	chr5:59902200-59924800	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:59909200-59927000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:59909400-59928800	Weak transcription	HMEC	breast
12	chr5:59910000-59921200	Weak transcription	Dnd41	blood
13	chr5:59910000-59925000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:59910000-59925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:59910800-59912000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:59910800-59912400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr5:59910800-59912400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
18	chr5:59911000-59911800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:59911000-59911800	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:59911000-59911800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:59911000-59911800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
22	chr5:59911000-59911800	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr5:59911000-59912200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr5:59911200-59911800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
25	chr5:59911400-59911800	ZNF genes & repeats	Placenta	Placenta

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