Variant report

Variant	rs12554953
Chromosome Location	chr9:8368253-8368254
allele	C/T
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:23)

rs_ID	r²[population]
rs10511493	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10976946	0.81[CHB][hapmap]
rs12552493	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs12555585	0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12682697	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12682993	0.86[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12684395	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1500315	0.85[CHB][hapmap]
rs16927547	0.95[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap]
rs20514	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3739578	0.86[CEU][hapmap];0.81[CHB][hapmap]
rs3780336	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap]
rs3847288	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3847291	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap]
rs4742486	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4742487	0.81[CHB][hapmap]
rs6477299	0.81[JPT][hapmap]
rs72691027	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72691034	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72691035	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7848626	0.81[CHB][hapmap]
rs7848705	0.86[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs7848818	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv892225	chr9:8345072-8379313	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12554953	HSD17B7P2	trans	cerebellum	SCAN
rs12554953	FIG4	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8341800-8372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:8350200-8372400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:8357200-8374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:8357600-8381800	Weak transcription	Aorta	Aorta
6	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:8364600-8370400	Weak transcription	Fetal Lung	lung
8	chr9:8364600-8382200	Weak transcription	Ovary	ovary
9	chr9:8364800-8376000	Weak transcription	Fetal Brain Male	brain
10	chr9:8364800-8377200	Weak transcription	Fetal Brain Female	brain
11	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
12	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:8365200-8386800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:8365600-8376600	Weak transcription	Brain Substantia Nigra	brain
15	chr9:8365600-8386200	Weak transcription	Brain Angular Gyrus	brain
16	chr9:8365600-8386200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:8365800-8375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:8366800-8370200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:8366800-8373000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:8366800-8383000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:8367000-8371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:8367200-8394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:8367600-8376200	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links