Variant report

Variant	rs62384476
Chromosome Location	chr5:115649509-115649510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115647669..115649812-chr5:115683571..115685304,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10035646	0.91[EUR][1000 genomes]
rs10036292	1.00[EUR][1000 genomes]
rs10040345	0.91[EUR][1000 genomes]
rs10042278	0.91[EUR][1000 genomes]
rs10043228	1.00[EUR][1000 genomes]
rs10051240	0.96[EUR][1000 genomes]
rs10052306	0.91[EUR][1000 genomes]
rs10054248	0.98[EUR][1000 genomes]
rs10063296	0.91[EUR][1000 genomes]
rs10073364	1.00[EUR][1000 genomes]
rs10079089	0.91[EUR][1000 genomes]
rs10079394	1.00[EUR][1000 genomes]
rs10155600	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10519448	0.96[EUR][1000 genomes]
rs12152964	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12153338	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153717	0.96[EUR][1000 genomes]
rs12153778	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12332489	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12332585	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12332658	0.96[EUR][1000 genomes]
rs12515251	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12515466	1.00[EUR][1000 genomes]
rs12519989	0.96[EUR][1000 genomes]
rs12520568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12520613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12520632	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12521440	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12521612	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12522027	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12522441	0.91[EUR][1000 genomes]
rs12523347	0.96[EUR][1000 genomes]
rs13362043	0.98[EUR][1000 genomes]
rs1382339	0.96[EUR][1000 genomes]
rs1422500	0.96[EUR][1000 genomes]
rs1592917	0.96[EUR][1000 genomes]
rs17139192	0.96[EUR][1000 genomes]
rs17139193	0.96[EUR][1000 genomes]
rs17139224	0.96[EUR][1000 genomes]
rs17139265	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17139314	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17139457	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35696109	0.91[EUR][1000 genomes]
rs4283834	0.91[EUR][1000 genomes]
rs4398671	0.96[EUR][1000 genomes]
rs59447169	0.91[EUR][1000 genomes]
rs62384189	0.87[EUR][1000 genomes]
rs62384212	0.91[EUR][1000 genomes]
rs62384213	0.91[EUR][1000 genomes]
rs62384215	0.91[EUR][1000 genomes]
rs62384229	0.91[EUR][1000 genomes]
rs62384230	0.91[EUR][1000 genomes]
rs62384231	0.91[EUR][1000 genomes]
rs62384233	0.91[EUR][1000 genomes]
rs62384235	0.91[EUR][1000 genomes]
rs62384236	0.91[EUR][1000 genomes]
rs62384237	0.96[EUR][1000 genomes]
rs62384238	0.96[EUR][1000 genomes]
rs62384250	0.91[EUR][1000 genomes]
rs62384253	0.91[EUR][1000 genomes]
rs62384461	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62384468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62384469	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384471	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384477	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384491	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62385975	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62385980	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62385993	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6876972	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6880880	0.96[EUR][1000 genomes]
rs7443669	0.91[EUR][1000 genomes]
rs7703121	0.83[ASN][1000 genomes]
rs7727882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62384476	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs62384476	COMMD10	cis	Muscle Skeletal	GTEx

Chromatin state (count:79 , 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	chr5:115641000-115653000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:115641400-115651800	Weak transcription	Esophagus	oesophagus
5	chr5:115642000-115654200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:115642400-115653000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:115642600-115654400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:115642800-115650800	Weak transcription	A549	lung
9	chr5:115642800-115655800	Weak transcription	Fetal Thymus	thymus
10	chr5:115643000-115653000	Weak transcription	Right Ventricle	heart
11	chr5:115643000-115656800	Weak transcription	Gastric	stomach
12	chr5:115643200-115650200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:115643200-115660200	Weak transcription	Placenta	Placenta
14	chr5:115643200-115664200	Weak transcription	Thymus	Thymus
15	chr5:115643200-115664800	Weak transcription	Pancreas	Pancrea
16	chr5:115643200-115669800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:115644000-115658600	Weak transcription	HSMM	muscle
18	chr5:115644200-115653200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:115644200-115655800	Weak transcription	HUVEC	blood vessel
20	chr5:115644400-115653000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:115644400-115653200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:115644400-115654200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:115644400-115664800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:115644400-115671800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:115645000-115651200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:115645000-115653000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:115645200-115653000	Weak transcription	Lung	lung
28	chr5:115645200-115653000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:115645400-115649800	Weak transcription	Aorta	Aorta
30	chr5:115645400-115650000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:115645400-115650200	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:115645600-115650000	Weak transcription	Primary B cells from cord blood	blood
33	chr5:115645600-115650000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:115645600-115651800	Weak transcription	Left Ventricle	heart
35	chr5:115645600-115652600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr5:115645600-115653400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:115646000-115653000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:115646400-115653200	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:115646400-115656000	Weak transcription	Fetal Kidney	kidney
40	chr5:115646600-115651800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr5:115647000-115653000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:115647200-115650800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr5:115647200-115653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:115647400-115652800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr5:115647600-115660400	Weak transcription	Small Intestine	intestine
46	chr5:115648200-115650200	Weak transcription	Ovary	ovary
47	chr5:115648400-115650200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:115648400-115651800	Weak transcription	Fetal Intestine Small	intestine
49	chr5:115648400-115653000	Weak transcription	Fetal Intestine Large	intestine
50	chr5:115648400-115653000	Weak transcription	Spleen	Spleen

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