Variant report

Variant	rs1876673
Chromosome Location	chr5:115450773-115450774
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10051697	0.88[ASN][1000 genomes]
rs10055868	0.88[ASN][1000 genomes]
rs10062350	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066259	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069656	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10478276	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10478277	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478278	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10478281	0.88[ASN][1000 genomes]
rs11241356	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514600	0.88[ASN][1000 genomes]
rs12514785	0.88[ASN][1000 genomes]
rs12515308	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516100	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12517508	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520076	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521815	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357258	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1581024	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17138884	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17138907	0.88[ASN][1000 genomes]
rs17138917	0.88[ASN][1000 genomes]
rs1876674	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661323	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28839012	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532392	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62383956	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62383957	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384678	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384691	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384692	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384693	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384695	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384697	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384699	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384700	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384714	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384716	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385177	0.88[ASN][1000 genomes]
rs62385178	0.88[ASN][1000 genomes]
rs62385179	0.88[ASN][1000 genomes]
rs62385215	0.88[ASN][1000 genomes]
rs6880213	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326989	0.88[ASN][1000 genomes]
rs9326990	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949677	chr5:115104829-115496168	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv599479	chr5:115233116-115450969	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv882736	chr5:115254723-115552945	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv882737	chr5:115263853-115552945	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	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
6	nsv527320	chr5:115382097-115573543	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv1027266	chr5:115382704-115501792	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	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
9	nsv1032199	chr5:115384131-115525738	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	esv2830404	chr5:115386661-115490546	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1019972	chr5:115386860-115563533	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv537869	chr5:115386860-115563533	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv1018861	chr5:115397834-115563533	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv537870	chr5:115397834-115563533	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	esv2762538	chr5:115436508-115455707	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1876673	COMMD10	cis	Muscle Skeletal	GTEx
rs1876673	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115433600-115457200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:115441000-115451200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:115444400-115456800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr5:115444800-115451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:115448400-115456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:115449000-115450800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:115449000-115466000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:115449200-115457600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:115449400-115465600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:115449600-115450800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
11	chr5:115449800-115450800	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr5:115449800-115451200	Enhancers	Pancreas	Pancrea
13	chr5:115450000-115451000	Strong transcription	Ovary	ovary
14	chr5:115450000-115451000	Enhancers	Right Ventricle	heart
15	chr5:115450000-115454800	Weak transcription	Dnd41	blood
16	chr5:115450000-115455800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr5:115450000-115455800	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr5:115450000-115473400	Weak transcription	Fetal Lung	lung
19	chr5:115450200-115451000	Enhancers	Left Ventricle	heart
20	chr5:115450200-115451400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:115450200-115455200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:115450200-115469600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:115450400-115451000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr5:115450400-115451000	Weak transcription	Gastric	stomach
25	chr5:115450400-115451200	Strong transcription	Primary B cells from cord blood	blood
26	chr5:115450400-115451800	Weak transcription	Spleen	Spleen
27	chr5:115450400-115454600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr5:115450400-115455600	Weak transcription	Fetal Stomach	stomach
29	chr5:115450600-115451400	Enhancers	Fetal Heart	heart
30	chr5:115450600-115451800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:115450600-115454600	Weak transcription	Primary T cells from cord blood	blood
32	chr5:115450600-115455200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:115450600-115457800	Weak transcription	Aorta	Aorta
34	chr5:115450600-115458800	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links