Variant report

Variant	rs11564410
Chromosome Location	chr18:25634094-25634095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11083244	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083247	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564295	0.86[CEU][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs11564298	0.89[YRI][hapmap]
rs11564398	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564401	0.95[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11564403	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564414	0.86[CEU][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11564418	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs11664205	0.86[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11664343	0.86[CEU][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs1220027	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12454980	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956425	0.81[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12957702	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12957780	0.86[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12971156	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1550662	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468213	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17468261	0.86[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17468415	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468443	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17468699	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761996	chr18:24866083-25818618	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv833605	chr18:25467096-25643447	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11564410	C18orf16	cis	parietal	SCAN
rs11564410	RIOK3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:25625800-25643400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr18:25625800-25650400	Weak transcription	Right Atrium	heart
3	chr18:25626000-25643200	Weak transcription	HUVEC	blood vessel
4	chr18:25627600-25645600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr18:25629400-25643000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr18:25630000-25634200	Weak transcription	Brain Substantia Nigra	brain
7	chr18:25630000-25643200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr18:25630000-25643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr18:25630200-25642400	Weak transcription	HSMM	muscle
10	chr18:25630400-25637600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr18:25630800-25634600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr18:25630800-25641200	Weak transcription	Left Ventricle	heart
13	chr18:25631600-25639200	Weak transcription	Osteobl	bone
14	chr18:25632000-25636200	Weak transcription	Fetal Heart	heart
15	chr18:25633000-25640400	Weak transcription	NH-A	brain
16	chr18:25633200-25636600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:25633800-25634200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
18	chr18:25633800-25635200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr18:25634000-25634200	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links