Variant report

Variant	rs6876972
Chromosome Location	chr5:115642519-115642520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115641553-115642622	NONHSAT103359

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10035646	0.89[EUR][1000 genomes]
rs10036292	0.98[EUR][1000 genomes]
rs10040345	0.89[EUR][1000 genomes]
rs10042278	0.89[EUR][1000 genomes]
rs10043228	0.98[EUR][1000 genomes]
rs10051240	0.93[EUR][1000 genomes]
rs10052306	0.89[EUR][1000 genomes]
rs10054248	0.96[EUR][1000 genomes]
rs10063296	0.89[EUR][1000 genomes]
rs10073364	0.98[EUR][1000 genomes]
rs10079089	0.89[EUR][1000 genomes]
rs10079394	0.98[EUR][1000 genomes]
rs10155600	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10478288	0.85[EUR][1000 genomes]
rs10519448	0.93[EUR][1000 genomes]
rs12152964	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153338	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12153717	0.93[EUR][1000 genomes]
rs12153778	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12332489	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332585	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12332658	0.93[EUR][1000 genomes]
rs12514110	0.83[ASN][1000 genomes]
rs12515251	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515466	0.98[EUR][1000 genomes]
rs12519989	0.93[EUR][1000 genomes]
rs12520568	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520613	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12520632	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12521440	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521612	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522027	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12522441	0.89[EUR][1000 genomes]
rs12523347	0.93[EUR][1000 genomes]
rs13362043	0.96[EUR][1000 genomes]
rs1382339	0.93[EUR][1000 genomes]
rs1422500	0.93[EUR][1000 genomes]
rs1592917	0.93[EUR][1000 genomes]
rs17139192	0.93[EUR][1000 genomes]
rs17139193	0.93[EUR][1000 genomes]
rs17139224	0.93[EUR][1000 genomes]
rs17139265	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17139314	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17139457	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35696109	0.89[EUR][1000 genomes]
rs4283834	0.89[EUR][1000 genomes]
rs4398671	0.93[EUR][1000 genomes]
rs59447169	0.89[EUR][1000 genomes]
rs62384184	0.85[EUR][1000 genomes]
rs62384186	0.85[EUR][1000 genomes]
rs62384187	0.81[EUR][1000 genomes]
rs62384189	0.85[EUR][1000 genomes]
rs62384212	0.89[EUR][1000 genomes]
rs62384213	0.89[EUR][1000 genomes]
rs62384215	0.89[EUR][1000 genomes]
rs62384229	0.89[EUR][1000 genomes]
rs62384230	0.89[EUR][1000 genomes]
rs62384231	0.89[EUR][1000 genomes]
rs62384233	0.89[EUR][1000 genomes]
rs62384235	0.89[EUR][1000 genomes]
rs62384236	0.89[EUR][1000 genomes]
rs62384237	0.93[EUR][1000 genomes]
rs62384238	0.93[EUR][1000 genomes]
rs62384250	0.89[EUR][1000 genomes]
rs62384253	0.89[EUR][1000 genomes]
rs62384461	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384468	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62384469	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384471	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62384476	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384477	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62384491	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62385975	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62385980	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62385993	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6880880	0.93[EUR][1000 genomes]
rs7443669	0.89[EUR][1000 genomes]
rs7727882	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[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
rs6876972	COMMD10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
5	chr5:115632000-115643000	Weak transcription	NH-A	brain
6	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
7	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
8	chr5:115634200-115643600	Weak transcription	HepG2	liver
9	chr5:115634200-115664400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:115634400-115645600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:115635400-115642600	Strong transcription	Left Ventricle	heart
12	chr5:115635400-115643600	Strong transcription	Fetal Intestine Large	intestine
13	chr5:115636200-115643600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr5:115637600-115643400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr5:115637600-115643800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:115637800-115642800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:115638200-115642600	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:115638200-115642800	Strong transcription	Pancreas	Pancrea
19	chr5:115638400-115643000	Strong transcription	Right Ventricle	heart
20	chr5:115638400-115643400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:115638400-115644000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:115638800-115643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:115639000-115644400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:115639200-115643200	Strong transcription	Placenta	Placenta
25	chr5:115639400-115642800	Strong transcription	A549	lung
26	chr5:115639400-115643000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:115639400-115645200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
28	chr5:115639600-115642800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr5:115639600-115643000	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:115639600-115643600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr5:115639600-115647400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:115639800-115642600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
33	chr5:115639800-115643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:115639800-115643400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr5:115640000-115644200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:115640200-115642600	Strong transcription	HSMMtube	muscle
37	chr5:115640200-115643600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr5:115640200-115645600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr5:115640200-115647200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr5:115640400-115643000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:115640400-115643000	ZNF genes & repeats	Fetal Intestine Small	intestine
42	chr5:115640400-115643200	ZNF genes & repeats	Aorta	Aorta
43	chr5:115640400-115643400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:115640400-115643400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
45	chr5:115640400-115643600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr5:115640400-115644400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
47	chr5:115640400-115644400	ZNF genes & repeats	Dnd41	blood
48	chr5:115640400-115645800	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr5:115640600-115643200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:115640600-115643200	Strong transcription	Thymus	Thymus

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