Variant report

Variant	rs62385980
Chromosome Location	chr5:115592908-115592909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10035646	0.91[EUR][1000 genomes]
rs10036292	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10040345	0.91[EUR][1000 genomes]
rs10042278	0.91[EUR][1000 genomes]
rs10043228	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051240	0.96[EUR][1000 genomes]
rs10052306	0.91[EUR][1000 genomes]
rs10054248	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056936	0.83[EUR][1000 genomes]
rs10063296	0.91[EUR][1000 genomes]
rs10073364	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079089	0.91[EUR][1000 genomes]
rs10079394	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155600	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10478288	0.87[EUR][1000 genomes]
rs10519448	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12152964	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153338	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12153717	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12153778	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12332489	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332585	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332658	0.96[EUR][1000 genomes]
rs12514110	0.83[ASN][1000 genomes]
rs12514600	0.86[AFR][1000 genomes]
rs12514785	0.86[AFR][1000 genomes]
rs12515251	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12515466	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519989	0.96[EUR][1000 genomes]
rs12520568	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520613	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520838	0.83[EUR][1000 genomes]
rs12521440	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12521612	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522027	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522441	0.91[EUR][1000 genomes]
rs12523347	0.96[EUR][1000 genomes]
rs13362043	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1382339	0.96[EUR][1000 genomes]
rs1422500	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1592917	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17139192	0.96[EUR][1000 genomes]
rs17139193	0.96[EUR][1000 genomes]
rs17139224	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17139265	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17139314	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17139457	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2136208	0.83[EUR][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]
rs62383957	0.86[AFR][1000 genomes]
rs62384181	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62384184	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62384186	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62384187	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs62384189	0.87[EUR][1000 genomes]
rs62384212	0.91[EUR][1000 genomes]
rs62384213	0.91[EUR][1000 genomes]
rs62384215	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62384229	0.91[EUR][1000 genomes]
rs62384230	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62384231	0.91[EUR][1000 genomes]
rs62384233	0.91[EUR][1000 genomes]
rs62384235	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62384236	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62384237	0.96[EUR][1000 genomes]
rs62384238	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62384250	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62384253	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62384461	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384468	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384469	0.90[EUR][1000 genomes]
rs62384471	0.88[EUR][1000 genomes]
rs62384476	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62384477	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62384491	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62385975	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62385993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6876972	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6880880	0.96[EUR][1000 genomes]
rs7443669	0.91[EUR][1000 genomes]
rs7727882	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9326994	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 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	nsv882743	chr5:115501792-115634127	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1019540	chr5:115526349-115610020	Weak transcription ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv2752058	chr5:115533065-115605198	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1016585	chr5:115533065-115605455	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1032799	chr5:115533065-115609552	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1016924	chr5:115533065-115610020	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv599481	chr5:115540041-115609552	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1024670	chr5:115540586-115615459	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv462401	chr5:115541563-115609552	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv599482	chr5:115541563-115609552	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv521050	chr5:115541563-115617297	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv599483	chr5:115561128-115609552	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv882744	chr5:115561128-115609552	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv882745	chr5:115561128-115616288	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	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
18	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
19	esv34428	chr5:115575513-115626966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv2753795	chr5:115576026-115626966	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv2755740	chr5:115576139-115633474	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	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
23	esv2757134	chr5:115578810-115633474	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	esv2759372	chr5:115578810-115633474	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	esv2760969	chr5:115583627-115630890	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
26	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
27	nsv1018714	chr5:115586834-115625245	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62385980	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs62385980	COMMD10	cis	Muscle Skeletal	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115560400-115610600	Weak transcription	Left Ventricle	heart
2	chr5:115579600-115610600	Weak transcription	Primary B cells from cord blood	blood
3	chr5:115582600-115594600	Weak transcription	Fetal Intestine Large	intestine
4	chr5:115584800-115603600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:115585800-115601200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:115586600-115595600	Weak transcription	Aorta	Aorta
7	chr5:115586600-115603000	Weak transcription	Dnd41	blood
8	chr5:115586800-115597000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:115586800-115608000	Weak transcription	Adipose Nuclei	Adipose
10	chr5:115586800-115609800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:115586800-115610800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:115587000-115599800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:115590800-115610200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr5:115591000-115607200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr5:115592000-115599600	Weak transcription	Primary T cells from cord blood	blood
16	chr5:115592000-115607800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:115592200-115593400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:115592800-115593200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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