Variant report

Variant	rs10054989
Chromosome Location	chr5:115663125-115663126
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]
rs10519454	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10519455	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12152996	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518094	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12518933	0.84[ASN][1000 genomes]
rs12521345	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12521635	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1529443	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1582430	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2068456	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57434520	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62384474	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62384478	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384495	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6866938	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6873096	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6873950	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7711510	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7717207	0.81[ASN][1000 genomes]
rs7717618	0.81[ASN][1000 genomes]
rs7717693	0.81[ASN][1000 genomes]
rs7721593	0.84[AMR][1000 genomes];1.00[ASN][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	esv34146	chr5:115315944-115729919	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv2755349	chr5:115384101-115733101	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv882746	chr5:115566026-115704566	Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017983	chr5:115578765-115713688	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv882748	chr5:115584159-115669950	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv869754	chr5:115634234-115696094	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv4968	chr5:115635771-115714856	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10054989	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:115643200-115664200	Weak transcription	Thymus	Thymus
3	chr5:115643200-115664800	Weak transcription	Pancreas	Pancrea
4	chr5:115643200-115669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:115644400-115664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
8	chr5:115649200-115663200	Weak transcription	HSMMtube	muscle
9	chr5:115652000-115665000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:115652000-115668000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:115653000-115667400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:115653400-115664600	Weak transcription	Psoas Muscle	Psoas
13	chr5:115653600-115670400	Weak transcription	Right Ventricle	heart
14	chr5:115654400-115664600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:115654600-115664400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:115654600-115664400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:115654600-115664800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr5:115654600-115665000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:115654600-115669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:115655200-115663800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr5:115655200-115664400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:115655400-115663800	Weak transcription	Lung	lung
23	chr5:115655400-115664400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:115655400-115669800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:115656400-115666400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr5:115657000-115663200	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:115657000-115664400	Weak transcription	Adipose Nuclei	Adipose
28	chr5:115657000-115665000	Weak transcription	Liver	Liver
29	chr5:115657400-115663800	Weak transcription	Primary T cells from cord blood	blood
30	chr5:115658800-115664800	Weak transcription	Ovary	ovary
31	chr5:115659200-115663800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr5:115659200-115663800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr5:115659200-115664200	Weak transcription	Dnd41	blood
34	chr5:115659200-115664600	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:115659200-115665000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:115659200-115669600	Weak transcription	Fetal Kidney	kidney
37	chr5:115659400-115663800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:115659400-115664200	Weak transcription	Primary B cells from cord blood	blood
39	chr5:115659400-115664200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:115660800-115664600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:115661200-115664800	Weak transcription	Left Ventricle	heart
42	chr5:115661400-115663800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:115661800-115664200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:115663000-115663400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

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