Variant report

Variant	rs963459
Chromosome Location	chr9:86507442-86507443
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10114889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10115699	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10125715	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868068	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10868070	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10868071	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10868076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11140251	0.88[CHB][hapmap]
rs11140253	0.88[CHB][hapmap]
rs11140265	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11140289	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11140304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12378956	0.94[CHB][hapmap]
rs12682981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs13290882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13296528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs167203	0.83[CEU][hapmap]
rs1831757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1889113	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1982151	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2378661	0.94[CHB][hapmap]
rs2576362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2780103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs295273	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs296886	0.82[CEU][hapmap]
rs296887	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs296888	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs296889	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs296890	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs296893	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3180887	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3818725	0.88[CHB][hapmap]
rs4147132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4147133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4535826	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6559751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7020300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7033292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7045126	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7047907	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7853254	0.83[AMR][1000 genomes]
rs7853377	0.83[CEU][hapmap]
rs7869321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9410888	0.88[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	esv2753071	chr9:86500946-86517546	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv972407	chr9:86501897-86517820	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
2	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86461600-86535400	Weak transcription	Ovary	ovary
4	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
5	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
6	chr9:86462800-86515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
8	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach
9	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:86482000-86518000	Weak transcription	Left Ventricle	heart
11	chr9:86490400-86510800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:86491400-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:86491800-86518200	Weak transcription	Primary B cells from cord blood	blood
16	chr9:86495000-86518000	Weak transcription	Primary T cells from cord blood	blood
17	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:86496400-86533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:86496600-86515600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:86499200-86513400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:86499400-86518200	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:86499400-86535000	Weak transcription	Fetal Kidney	kidney
23	chr9:86499800-86523200	Weak transcription	Fetal Thymus	thymus
24	chr9:86500000-86534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:86500200-86521200	Weak transcription	Adipose Nuclei	Adipose
26	chr9:86500200-86521200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:86500200-86535200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr9:86500200-86535200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:86500200-86535600	Weak transcription	Lung	lung
30	chr9:86501200-86514600	Weak transcription	HepG2	liver
31	chr9:86501200-86521600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:86501800-86512400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:86502000-86511600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:86502000-86532400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:86502600-86535000	Weak transcription	Fetal Lung	lung
36	chr9:86502800-86512400	Weak transcription	Brain Germinal Matrix	brain
37	chr9:86503000-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:86506400-86534800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links