Variant report

Variant	rs158385
Chromosome Location	chr10:43133320-43133321
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:147805816..147808650-chr10:43132811..43135125,2	MCF-7	breast:
2	chr10:43133014..43133804-chr19:8273425..8274342,2	NB4	blood:
3	chr10:43132954..43135205-chr10:43277445..43279937,2	K562	blood:
4	chr10:43100572..43103779-chr10:43131525..43135101,4	MCF-7	breast:
5	chr10:43132257..43135644-chr10:43275563..43280155,11	MCF-7	breast:
6	chr10:43046145..43048386-chr10:43132522..43135382,4	MCF-7	breast:
7	chr10:43126488..43130043-chr10:43132001..43133906,3	MCF-7	breast:
8	chr10:43124209..43130093-chr10:43131977..43134761,6	K562	blood:
9	chr10:43132863..43135217-chr10:43276470..43279459,4	K562	blood:
10	chr10:43125083..43130093-chr10:43132029..43136060,7	K562	blood:
11	chr10:43132020..43136600-chr10:43277441..43279853,5	MCF-7	breast:
12	chr10:43043951..43049889-chr10:43132519..43135803,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000251783	Chromatin interaction
ENSG00000234420	Chromatin interaction
ENSG00000165733	Chromatin interaction
ENSG00000090661	Chromatin interaction
ENSG00000272373	Chromatin interaction
ENSG00000202408	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs158373	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs158376	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs158384	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158389	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158390	0.85[ASN][1000 genomes]
rs158392	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210272	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs210278	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs210279	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs210284	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs210287	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2184238	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2473118	0.85[ASN][1000 genomes]
rs2484298	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs289182	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs289183	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs590937	0.86[ASN][1000 genomes]
rs668169	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs668649	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817455	chr10:42607635-43151812	Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv550672	chr10:42753190-43441729	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv895064	chr10:42783481-43243325	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv533331	chr10:42830221-43356410	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1042764	chr10:42846383-43511712	Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1050394	chr10:42890663-43604956	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv540573	chr10:42890663-43604956	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
9	nsv469725	chr10:42965130-43178323	Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv482513	chr10:42965130-43178323	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv2758216	chr10:42965131-43510191	Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
12	esv2759746	chr10:42965131-43510191	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv2757381	chr10:43104068-43352995	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	esv34929	chr10:43116194-43329770	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs158385	LINC00839	cis	lung	GTEx
rs158385	LINC00839	cis	Artery Aorta	GTEx
rs158385	LINC00839	cis	Artery Tibial	GTEx
rs158385	LINC00839	cis	Esophagus Mucosa	GTEx
rs158385	LINC00839	cis	Esophagus Muscularis	GTEx
rs158385	LINC00839	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43132000-43134800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr10:43132000-43134800	Active TSS	Brain Germinal Matrix	brain
3	chr10:43132200-43134400	Active TSS	Pancreas	Pancrea
4	chr10:43132400-43133400	Flanking Active TSS	Dnd41	blood
5	chr10:43132400-43133600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:43132400-43134600	Active TSS	Fetal Intestine Small	intestine
7	chr10:43132400-43134600	Active TSS	Fetal Kidney	kidney
8	chr10:43132400-43134600	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr10:43132400-43134800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr10:43132400-43134800	Active TSS	Fetal Intestine Large	intestine
11	chr10:43132400-43134800	Active TSS	HMEC	breast
12	chr10:43132600-43133400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:43132600-43133400	Flanking Active TSS	Fetal Heart	heart
14	chr10:43132600-43133600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr10:43132600-43133600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:43132600-43133600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr10:43132600-43134600	Active TSS	Duodenum Mucosa	Duodenum
18	chr10:43132600-43134800	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr10:43132600-43134800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr10:43132600-43134800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr10:43132600-43134800	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr10:43132600-43134800	Active TSS	A549	lung
23	chr10:43132800-43133400	Flanking Active TSS	Liver	Liver
24	chr10:43132800-43133400	Flanking Active TSS	Fetal Lung	lung
25	chr10:43132800-43133600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr10:43132800-43133800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:43132800-43134400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr10:43132800-43134400	Active TSS	Fetal Brain Male	brain
29	chr10:43132800-43134600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr10:43132800-43134600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:43132800-43134600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr10:43132800-43134600	Active TSS	Colonic Mucosa	Colon
33	chr10:43132800-43134600	Active TSS	Fetal Stomach	stomach
34	chr10:43132800-43134800	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr10:43133000-43133400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:43133000-43133400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr10:43133000-43133400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr10:43133000-43133400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr10:43133000-43133400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:43133000-43133400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr10:43133000-43133400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr10:43133000-43133400	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr10:43133000-43133400	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr10:43133000-43133400	Flanking Active TSS	Fetal Thymus	thymus
45	chr10:43133000-43133600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr10:43133000-43133600	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr10:43133000-43133600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
48	chr10:43133000-43133600	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr10:43133000-43133600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr10:43133000-43133600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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