Variant report

Variant	rs2570306
Chromosome Location	chr9:8843382-8843383
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1865341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865342	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865343	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2254372	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2254373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2570963	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2570306	CD274	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8823400-8845000	Weak transcription	Fetal Brain Female	brain
2	chr9:8833600-8845000	Weak transcription	Fetal Heart	heart
3	chr9:8835000-8850800	Weak transcription	Fetal Kidney	kidney
4	chr9:8835200-8852000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:8835200-8852400	Weak transcription	Aorta	Aorta
6	chr9:8835400-8845000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:8835600-8850800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:8835600-8851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:8835800-8844600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:8835800-8851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:8837400-8845400	Weak transcription	Ovary	ovary
12	chr9:8838200-8845000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:8839600-8845600	Enhancers	Brain Hippocampus Middle	brain
14	chr9:8840400-8843600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:8840600-8845600	Enhancers	Brain Substantia Nigra	brain
16	chr9:8841800-8845200	Enhancers	Brain Angular Gyrus	brain
17	chr9:8842200-8843400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr9:8842400-8843400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr9:8842400-8843600	Enhancers	Brain Germinal Matrix	brain
20	chr9:8842600-8843400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:8842600-8843400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:8842600-8843800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:8842800-8843600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr9:8842800-8843600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr9:8842800-8843600	Strong transcription	Fetal Lung	lung
26	chr9:8843000-8843400	Weak transcription	Fetal Brain Male	brain
27	chr9:8843000-8844800	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:8843000-8845600	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr9:8843000-8847000	Enhancers	Brain Cingulate Gyrus	brain
30	chr9:8843000-8852400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:8843000-8855200	Weak transcription	Fetal Stomach	stomach
32	chr9:8843000-8856600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:8843200-8844600	Weak transcription	Brain Anterior Caudate	brain
34	chr9:8843200-8846600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:8843200-8854200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links