Variant report

Variant	rs2123178
Chromosome Location	chr3:56288610-56288611
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11130505	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11718962	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12630006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12633004	0.82[EUR][1000 genomes]
rs13081402	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13081691	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17235466	0.83[EUR][1000 genomes]
rs17825368	0.81[EUR][1000 genomes]
rs34484508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4974188	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66697960	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6770399	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771628	0.80[EUR][1000 genomes]
rs6781843	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6783930	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794479	0.83[EUR][1000 genomes]
rs73086405	0.81[EUR][1000 genomes]
rs7640618	0.81[EUR][1000 genomes]
rs901151	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809991	0.80[EUR][1000 genomes]
rs9847090	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2123178	C3orf51	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56272800-56291400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:56286800-56288800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:56287000-56288800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:56287000-56288800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:56287400-56288800	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr3:56287600-56288800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:56287600-56289600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:56287600-56290200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:56287800-56289200	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:56288000-56288800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr3:56288200-56289400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:56288400-56289600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:56288400-56289800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:56288600-56288800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:56288600-56289000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:56288600-56289000	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links