Variant report

Variant	rs904781
Chromosome Location	chr9:8390006-8390007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1039337	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10739162	0.89[CHB][hapmap]
rs10758968	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10815870	0.89[CHB][hapmap]
rs10977029	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10977030	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10977060	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.81[ASN][1000 genomes]
rs12235640	0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12235754	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.85[ASN][1000 genomes]
rs13292038	1.00[CHB][hapmap]
rs1359114	0.89[CHB][hapmap]
rs1500326	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1500332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1500333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1535674	0.89[CHB][hapmap]
rs1535675	0.89[CHB][hapmap];0.97[CHD][hapmap]
rs2031214	0.89[CHB][hapmap];0.97[CHD][hapmap]
rs2031216	0.89[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap]
rs2031219	0.89[CHB][hapmap]
rs3847294	0.89[CHB][hapmap]
rs3896024	0.89[CHB][hapmap]
rs3901934	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap]
rs4742502	0.89[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap]
rs7027844	0.90[CHD][hapmap]
rs7036240	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.85[ASN][1000 genomes]
rs7042145	0.89[CHB][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs7849327	0.89[CHB][hapmap];0.82[GIH][hapmap]
rs7849657	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7856760	0.89[CHB][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	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
4	esv3350037	chr9:8389674-8390169	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs904781	CDC37L1	cis	cerebellum	SCAN
rs904781	CD274	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
4	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8367200-8394600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:8367200-8399800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:8373000-8402200	Weak transcription	Fetal Kidney	kidney
8	chr9:8374000-8394400	Weak transcription	Fetal Heart	heart
9	chr9:8376800-8393200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:8376800-8401800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:8377800-8406400	Weak transcription	Fetal Brain Female	brain
12	chr9:8383600-8405200	Weak transcription	Aorta	Aorta
13	chr9:8384200-8394600	Weak transcription	Left Ventricle	heart
14	chr9:8385200-8401400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:8387000-8394600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:8387200-8392600	Weak transcription	Fetal Lung	lung
17	chr9:8387600-8394800	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:8387800-8393400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:8387800-8393800	Weak transcription	Brain Angular Gyrus	brain
20	chr9:8387800-8393800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:8387800-8398800	Weak transcription	Ovary	ovary
22	chr9:8388000-8402000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:8388400-8394400	Weak transcription	Brain Anterior Caudate	brain
24	chr9:8389600-8451000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:8389800-8394800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links