Variant report

Variant	rs17139455
Chromosome Location	chr5:115640107-115640108
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1001014	0.83[JPT][hapmap]
rs10519454	0.88[CHD][hapmap]
rs11241379	0.81[JPT][hapmap]
rs17138925	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs17139182	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17139253	0.83[JPT][hapmap]
rs17139333	0.83[JPT][hapmap]
rs17139366	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs17139438	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17139495	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17139655	0.96[EUR][1000 genomes]
rs2068456	0.85[CHD][hapmap]
rs4921085	0.83[JPT][hapmap]
rs6866938	0.85[CHD][hapmap]
rs6888823	0.91[JPT][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	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	nsv882747	chr5:115566636-115662510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
rs17139455	COMMD10	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115613400-115641600	Weak transcription	HSMM	muscle
2	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
4	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
9	chr5:115631800-115640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:115631800-115641800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:115632000-115643000	Weak transcription	NH-A	brain
12	chr5:115632600-115640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:115632600-115640600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
15	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
16	chr5:115633200-115640800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:115633800-115640400	Weak transcription	Esophagus	oesophagus
18	chr5:115634000-115640400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:115634200-115640200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:115634200-115640400	Weak transcription	Fetal Intestine Small	intestine
21	chr5:115634200-115640600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:115634200-115640600	Weak transcription	Thymus	Thymus
23	chr5:115634200-115640800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:115634200-115640800	Weak transcription	Psoas Muscle	Psoas
25	chr5:115634200-115641400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr5:115634200-115641800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:115634200-115641800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:115634200-115642200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:115634200-115643600	Weak transcription	HepG2	liver
30	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:115634400-115640400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:115634400-115640400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:115634400-115640400	Weak transcription	Brain Anterior Caudate	brain
34	chr5:115634400-115640400	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:115634400-115640600	Strong transcription	Adipose Nuclei	Adipose
36	chr5:115634400-115640600	Weak transcription	GM12878-XiMat	blood
37	chr5:115634400-115641800	Strong transcription	Brain Substantia Nigra	brain
38	chr5:115634400-115645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:115634600-115640200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr5:115634600-115640800	Strong transcription	Primary B cells from cord blood	blood
41	chr5:115634600-115641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr5:115634800-115641200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr5:115635200-115640400	Strong transcription	Primary T cells from cord blood	blood
44	chr5:115635400-115642400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr5:115635400-115642600	Strong transcription	Left Ventricle	heart
46	chr5:115635400-115643600	Strong transcription	Fetal Intestine Large	intestine
47	chr5:115635600-115640400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:115635600-115640400	Weak transcription	Gastric	stomach
49	chr5:115635600-115640600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr5:115635600-115641600	Weak transcription	Brain Germinal Matrix	brain

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