Variant report

Variant	rs10815962
Chromosome Location	chr9:8822716-8822717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10758999	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10759000	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10815955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815956	1.00[CEU][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10815957	0.89[EUR][1000 genomes]
rs10815958	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10815963	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10815966	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10815967	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10815968	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10815969	0.84[EUR][1000 genomes]
rs10815970	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10977308	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10977309	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10977310	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10977312	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10977319	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1368980	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1865339	0.81[CHB][hapmap]
rs7037145	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7042203	0.93[CEU][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9918965	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv892240	chr9:8796449-8834108	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10815962	INSL4	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8794800-8825600	Weak transcription	Ovary	ovary
2	chr9:8808000-8825600	Weak transcription	Aorta	Aorta
3	chr9:8816600-8825200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:8817000-8832000	Weak transcription	Fetal Heart	heart
5	chr9:8817200-8823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:8817200-8824200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:8817200-8825000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:8817200-8831800	Weak transcription	Fetal Lung	lung
9	chr9:8817600-8822800	Weak transcription	Fetal Brain Female	brain
10	chr9:8817600-8823400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:8817600-8824000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:8817600-8826000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr9:8817800-8822800	Weak transcription	Brain Anterior Caudate	brain
14	chr9:8817800-8824200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:8818000-8824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:8818200-8823600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:8820600-8823600	Enhancers	Brain Substantia Nigra	brain
18	chr9:8821200-8823000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:8821400-8835000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:8821600-8823200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:8821600-8823400	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:8821600-8823800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:8821800-8823000	Active TSS	Liver	Liver
24	chr9:8822000-8825600	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:8822200-8823800	Enhancers	Brain Angular Gyrus	brain
26	chr9:8822200-8838600	Weak transcription	Osteobl	bone
27	chr9:8822400-8827200	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:8822600-8823000	Enhancers	Fetal Muscle Leg	muscle
29	chr9:8822600-8823200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr9:8822600-8823200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:8822600-8823200	Enhancers	Brain Cingulate Gyrus	brain

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