Variant report

Variant	rs62384474
Chromosome Location	chr5:115634018-115634019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:115630950..115633524-chr5:115633964..115636710,2	MCF-7	breast:
2	chr5:115632385..115634405-chr5:115635053..115637473,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-4	chr5:115633944-115634089	NONHSAT103358
2	lnc-LVRN.1-4	chr5:115633944-115634089	NONHSAT103359

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10054989	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10519454	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10519455	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12152996	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12518094	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12521345	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1582430	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2068456	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57434520	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62384478	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62384495	0.90[EUR][1000 genomes]
rs6866938	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873096	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6873950	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7711510	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7721593	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62384474	COMMD10	Cis_1M	lymphoblastoid	RTeQTL
rs62384474	COMMD10	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115613400-115641600	Weak transcription	HSMM	muscle
2	chr5:115625600-115639200	Weak transcription	Fetal Stomach	stomach
3	chr5:115625600-115643000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr5:115626600-115641600	Weak transcription	Fetal Brain Male	brain
5	chr5:115626800-115642200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:115627200-115635200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:115627800-115639200	Weak transcription	Placenta	Placenta
8	chr5:115628000-115643800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:115628400-115639200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:115628400-115641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:115628600-115639400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:115628600-115643400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:115629000-115643800	Weak transcription	HUVEC	blood vessel
14	chr5:115629400-115638200	Weak transcription	Pancreas	Pancrea
15	chr5:115629400-115638400	Weak transcription	Right Ventricle	heart
16	chr5:115631400-115636200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:115631400-115637800	Weak transcription	Fetal Thymus	thymus
18	chr5:115631800-115640600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:115631800-115641800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:115632000-115634200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
21	chr5:115632000-115634800	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr5:115632000-115639200	Weak transcription	Lung	lung
23	chr5:115632000-115643000	Weak transcription	NH-A	brain
24	chr5:115632200-115634600	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr5:115632200-115635600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:115632400-115634200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr5:115632600-115634600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr5:115632600-115640400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:115632600-115640600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr5:115632600-115643400	Weak transcription	Stomach Mucosa	stomach
31	chr5:115632800-115639600	Weak transcription	Brain Angular Gyrus	brain
32	chr5:115632800-115642600	Weak transcription	NHDF-Ad	bronchial
33	chr5:115633000-115634200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:115633000-115634600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr5:115633000-115634600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
36	chr5:115633000-115635800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:115633200-115634200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr5:115633200-115634200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
39	chr5:115633200-115634200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr5:115633200-115634200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
41	chr5:115633200-115634200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:115633200-115634200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr5:115633200-115634200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:115633200-115634200	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr5:115633200-115634200	ZNF genes & repeats	Left Ventricle	heart
46	chr5:115633200-115634200	ZNF genes & repeats	Psoas Muscle	Psoas
47	chr5:115633200-115634200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
48	chr5:115633200-115634200	ZNF genes & repeats	Dnd41	blood
49	chr5:115633200-115634400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr5:115633200-115634400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood

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