Variant report

Variant	rs712588
Chromosome Location	chr5:115654605-115654606
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1090078	0.83[ASN][1000 genomes]
rs12109104	0.83[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs1382343	0.81[ASN][1000 genomes]
rs1382344	0.81[ASN][1000 genomes]
rs149131	0.84[ASN][1000 genomes]
rs153580	0.89[ASN][1000 genomes]
rs153593	0.84[ASN][1000 genomes]
rs153594	0.84[ASN][1000 genomes]
rs1644268	0.83[ASN][1000 genomes]
rs1669135	0.81[ASN][1000 genomes]
rs1669136	0.85[JPT][hapmap]
rs1677406	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs185263	0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs253950	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs253951	0.83[ASN][1000 genomes]
rs253952	0.83[ASN][1000 genomes]
rs253959	0.83[CHB][hapmap]
rs254151	0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs254171	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs254172	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs254173	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs254174	0.83[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs27125	0.84[ASN][1000 genomes]
rs37180	0.81[ASN][1000 genomes]
rs40192	0.81[ASN][1000 genomes]
rs41271	0.81[ASN][1000 genomes]
rs712576	0.88[ASN][1000 genomes]
rs712577	0.87[ASN][1000 genomes]
rs712579	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712591	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs712592	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712593	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712594	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712595	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712596	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712597	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712598	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712599	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712601	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs784479	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs784481	0.81[ASN][1000 genomes]
rs785371	0.88[ASN][1000 genomes]
rs785373	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs785374	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785375	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs785377	0.86[ASN][1000 genomes]
rs803967	0.81[JPT][hapmap]
rs809210	0.81[ASN][1000 genomes]
rs810742	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
rs712588	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 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	chr5:115640800-115658200	Weak transcription	Colonic Mucosa	Colon
3	chr5:115642800-115655800	Weak transcription	Fetal Thymus	thymus
4	chr5:115643000-115656800	Weak transcription	Gastric	stomach
5	chr5:115643200-115660200	Weak transcription	Placenta	Placenta
6	chr5:115643200-115664200	Weak transcription	Thymus	Thymus
7	chr5:115643200-115664800	Weak transcription	Pancreas	Pancrea
8	chr5:115643200-115669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:115644000-115658600	Weak transcription	HSMM	muscle
10	chr5:115644200-115655800	Weak transcription	HUVEC	blood vessel
11	chr5:115644400-115664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:115646400-115656000	Weak transcription	Fetal Kidney	kidney
14	chr5:115647600-115660400	Weak transcription	Small Intestine	intestine
15	chr5:115648400-115655200	Weak transcription	Fetal Stomach	stomach
16	chr5:115649000-115692800	Weak transcription	Fetal Heart	heart
17	chr5:115649200-115663200	Weak transcription	HSMMtube	muscle
18	chr5:115649600-115656600	Weak transcription	Colon Smooth Muscle	Colon
19	chr5:115649600-115658000	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr5:115649800-115656000	Weak transcription	Liver	Liver
21	chr5:115650200-115655400	Strong transcription	Adipose Nuclei	Adipose
22	chr5:115650800-115659200	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:115651800-115655400	Strong transcription	Left Ventricle	heart
24	chr5:115652000-115656000	Weak transcription	Osteobl	bone
25	chr5:115652000-115665000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:115652000-115668000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:115652200-115655800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:115652600-115654800	Strong transcription	Duodenum Mucosa	Duodenum
29	chr5:115652600-115655200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
30	chr5:115652600-115655400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr5:115652800-115655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:115652800-115655400	Strong transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:115652800-115655800	Weak transcription	HepG2	liver
34	chr5:115652800-115656400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:115652800-115659400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:115653000-115654800	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr5:115653000-115655000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr5:115653000-115655200	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr5:115653000-115655400	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr5:115653000-115655600	Strong transcription	Fetal Lung	lung
41	chr5:115653000-115667400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:115653200-115655200	ZNF genes & repeats	Brain Hippocampus Middle	brain
43	chr5:115653200-115658800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr5:115653200-115659200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:115653400-115655200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:115653400-115655400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:115653400-115658200	Weak transcription	Esophagus	oesophagus
48	chr5:115653400-115658400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr5:115653400-115664600	Weak transcription	Psoas Muscle	Psoas
50	chr5:115653600-115654800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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