Variant report

Variant	rs785375
Chromosome Location	chr5:115659452-115659453
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10042177	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs10051072	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs10051302	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs10056823	1.00[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10063312	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs10066081	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs10077013	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs10078121	0.82[CHB][hapmap]
rs10079466	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs10079691	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs1090077	0.82[EUR][1000 genomes]
rs1090078	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11241374	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs11241375	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs11742938	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs12054994	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs12109104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12657249	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs13159102	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs13161987	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs1382343	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1382344	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396481	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs1396482	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs149131	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1508875	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs153588	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs153593	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs153594	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567335	0.86[CEU][hapmap]
rs1644268	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669135	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669136	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1677405	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1677406	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1677415	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs173813	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs173834	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs185263	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs253950	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs253951	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs253952	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs253955	0.84[AMR][1000 genomes]
rs253959	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs253961	0.83[ASN][1000 genomes]
rs254150	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs254151	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs254152	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs254171	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs254172	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs254173	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs254174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27125	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27126	0.84[ASN][1000 genomes]
rs27368	0.85[ASN][1000 genomes]
rs28031	0.85[ASN][1000 genomes]
rs37180	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40192	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41271	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42959	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6594948	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs6861437	0.87[ASN][1000 genomes]
rs712561	0.95[CEU][hapmap];0.87[CHB][hapmap]
rs712574	0.87[ASN][1000 genomes]
rs712579	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs712588	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs712591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs712592	0.87[ASN][1000 genomes]
rs712593	0.87[ASN][1000 genomes]
rs712594	0.87[ASN][1000 genomes]
rs712595	0.87[ASN][1000 genomes]
rs712596	0.87[ASN][1000 genomes]
rs712597	0.87[ASN][1000 genomes]
rs712598	0.87[ASN][1000 genomes]
rs712599	0.87[ASN][1000 genomes]
rs712600	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs712601	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7723358	1.00[CEU][hapmap]
rs7735539	1.00[CEU][hapmap];0.91[CHB][hapmap]
rs784479	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs784481	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs785367	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs785369	0.87[ASN][1000 genomes]
rs785370	0.87[ASN][1000 genomes]
rs785373	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs785374	0.87[ASN][1000 genomes]
rs785377	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs803967	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs804151	0.81[AMR][1000 genomes]
rs809188	0.82[EUR][1000 genomes]
rs809210	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs810742	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs929752	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv1018001	chr5:115640603-115660285	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs785375	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:115643200-115660200	Weak transcription	Placenta	Placenta
3	chr5:115643200-115664200	Weak transcription	Thymus	Thymus
4	chr5:115643200-115664800	Weak transcription	Pancreas	Pancrea
5	chr5:115643200-115669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:115644400-115664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:115647600-115660400	Weak transcription	Small Intestine	intestine
9	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
10	chr5:115649200-115663200	Weak transcription	HSMMtube	muscle
11	chr5:115652000-115665000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr5:115652000-115668000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:115653000-115667400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:115653400-115664600	Weak transcription	Psoas Muscle	Psoas
15	chr5:115653600-115660000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:115653600-115670400	Weak transcription	Right Ventricle	heart
17	chr5:115654400-115661000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:115654400-115664600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:115654600-115664400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:115654600-115664400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:115654600-115664800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:115654600-115665000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:115654600-115669600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:115655000-115660000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:115655200-115659800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:115655200-115663800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:115655200-115664400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:115655400-115663800	Weak transcription	Lung	lung
29	chr5:115655400-115664400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:115655400-115669800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:115656400-115666400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr5:115657000-115663200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr5:115657000-115664400	Weak transcription	Adipose Nuclei	Adipose
34	chr5:115657000-115665000	Weak transcription	Liver	Liver
35	chr5:115657400-115663800	Weak transcription	Primary T cells from cord blood	blood
36	chr5:115657600-115660800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:115658200-115660400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr5:115658400-115663000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:115658800-115660400	Weak transcription	Left Ventricle	heart
40	chr5:115658800-115664800	Weak transcription	Ovary	ovary
41	chr5:115659200-115659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:115659200-115660200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:115659200-115663800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr5:115659200-115663800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr5:115659200-115664200	Weak transcription	Dnd41	blood
46	chr5:115659200-115664600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:115659200-115665000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr5:115659200-115669600	Weak transcription	Fetal Kidney	kidney
49	chr5:115659400-115659800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr5:115659400-115660400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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