Variant report

Variant	rs2198865
Chromosome Location	chr5:59954057-59954058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10939855	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939856	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11739724	0.85[ASN][1000 genomes]
rs11741754	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11948543	0.96[ASN][1000 genomes]
rs11951503	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11951950	0.87[ASN][1000 genomes]
rs11952735	0.96[ASN][1000 genomes]
rs11955398	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11956023	0.98[ASN][1000 genomes]
rs11959922	0.98[ASN][1000 genomes]
rs12517174	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12517207	0.81[EUR][1000 genomes]
rs12522801	0.80[ASN][1000 genomes]
rs1379115	0.81[ASN][1000 genomes]
rs1379116	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1379117	0.99[ASN][1000 genomes]
rs153152	0.84[EUR][1000 genomes]
rs1562235	0.89[ASN][1000 genomes]
rs17387940	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2061250	0.95[ASN][1000 genomes]
rs248912	0.85[EUR][1000 genomes]
rs249070	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2591636	0.93[ASN][1000 genomes]
rs286153	0.96[ASN][1000 genomes]
rs286154	0.82[ASN][1000 genomes]
rs286155	0.96[ASN][1000 genomes]
rs286156	0.90[ASN][1000 genomes]
rs286158	0.90[ASN][1000 genomes]
rs2898287	0.89[ASN][1000 genomes]
rs3857236	0.94[ASN][1000 genomes]
rs3958943	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4504343	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4538566	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4700378	0.81[ASN][1000 genomes]
rs4700379	0.83[ASN][1000 genomes]
rs4700380	0.95[ASN][1000 genomes]
rs4700381	0.88[ASN][1000 genomes]
rs5012862	0.82[ASN][1000 genomes]
rs55720622	0.86[ASN][1000 genomes]
rs55768631	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56137970	0.85[ASN][1000 genomes]
rs56166952	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56191602	1.00[ASN][1000 genomes]
rs56347749	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56726435	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59155887	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62372964	0.87[ASN][1000 genomes]
rs62373023	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6877561	0.90[ASN][1000 genomes]
rs6896942	0.80[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2198865	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs2198865	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 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	chr5:59954000-59954400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
17	chr5:59954000-59955400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:59954000-59961800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:59954000-59980200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links