Variant report

Variant	rs11660291
Chromosome Location	chr18:45522194-45522195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11661805	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12454831	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12456505	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12458978	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12959163	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12971176	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13381433	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17885999	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28679354	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34380210	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36033209	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55670531	0.95[ASN][1000 genomes]
rs61022371	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62087556	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62087557	0.84[ASN][1000 genomes]
rs7236676	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7504201	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7504245	0.96[CEU][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9948382	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9950547	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9967472	0.88[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	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1066479	chr18:45505569-45554507	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1055669	chr18:45513090-45559375	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11660291	ZBTB7C	cis	cerebellum	SCAN
rs11660291	MYO5B	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45510400-45523600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr18:45516000-45523800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr18:45516200-45527600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr18:45517600-45529000	Weak transcription	Right Ventricle	heart
5	chr18:45517800-45522400	Weak transcription	Fetal Muscle Leg	muscle
6	chr18:45519600-45522400	Weak transcription	Brain Germinal Matrix	brain
7	chr18:45520000-45522200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr18:45520400-45529600	Weak transcription	Stomach Mucosa	stomach
9	chr18:45521000-45523600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr18:45521200-45522400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr18:45521200-45522800	Weak transcription	Fetal Kidney	kidney
12	chr18:45521200-45526200	Weak transcription	Hela-S3	cervix
13	chr18:45521400-45523400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:45521800-45523400	Enhancers	HSMM	muscle
15	chr18:45521800-45523400	Enhancers	HSMMtube	muscle
16	chr18:45521800-45523600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:45522000-45522400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:45522000-45523000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr18:45522000-45523000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links