Variant report

Variant	rs1255392
Chromosome Location	chr10:43021089-43021090
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1147916	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1147917	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1147918	0.81[AFR][1000 genomes]
rs1147919	0.81[AFR][1000 genomes]
rs1255369	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255370	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255385	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255386	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1255387	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1255395	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1255396	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255401	0.85[EUR][1000 genomes]
rs1255414	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2473112	0.81[AFR][1000 genomes]
rs2473115	0.81[AFR][1000 genomes]
rs2504025	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv550670	chr10:42725663-43089965	Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	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
4	nsv895054	chr10:42761931-43068841	ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	nsv466877	chr10:42794125-43066414	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv550683	chr10:42794125-43066414	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv895071	chr10:42864138-43066414	ZNF genes & repeats Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv895073	chr10:42884169-43066505	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1255392	LINC00839	cis	lung	GTEx
rs1255392	LINC00839	cis	Artery Tibial	GTEx
rs1255392	LINC00839	cis	Artery Aorta	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43009200-43021600	ZNF genes & repeats	Liver	Liver
2	chr10:43009200-43021600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr10:43012400-43021600	ZNF genes & repeats	Primary T cells from cord blood	blood
4	chr10:43012400-43021600	ZNF genes & repeats	Colon Smooth Muscle	Colon
5	chr10:43013200-43021600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr10:43013400-43021200	ZNF genes & repeats	Fetal Brain Female	brain
7	chr10:43013400-43021600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:43014600-43021600	ZNF genes & repeats	Fetal Lung	lung
9	chr10:43014800-43021600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr10:43014800-43021600	ZNF genes & repeats	Psoas Muscle	Psoas
11	chr10:43014800-43021600	ZNF genes & repeats	Dnd41	blood
12	chr10:43015200-43021600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
13	chr10:43015200-43021600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
14	chr10:43015400-43021200	ZNF genes & repeats	Fetal Brain Male	brain
15	chr10:43015400-43021600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
16	chr10:43015400-43021600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
17	chr10:43015400-43021600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:43015600-43021600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
19	chr10:43015600-43021600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr10:43016200-43022000	Weak transcription	HepG2	liver
21	chr10:43018000-43021600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:43018200-43021400	Strong transcription	Placenta	Placenta
23	chr10:43018200-43022400	Weak transcription	HSMMtube	muscle
24	chr10:43019400-43021200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr10:43019600-43034400	Weak transcription	Fetal Thymus	thymus
26	chr10:43020000-43021200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr10:43020000-43021200	ZNF genes & repeats	Fetal Stomach	stomach
28	chr10:43020000-43021200	ZNF genes & repeats	Left Ventricle	heart
29	chr10:43020200-43021600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr10:43020400-43021600	Strong transcription	Brain Angular Gyrus	brain
31	chr10:43020400-43022000	Weak transcription	A549	lung
32	chr10:43020400-43024400	Weak transcription	GM12878-XiMat	blood
33	chr10:43020400-43047000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr10:43020600-43021400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr10:43020600-43021800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr10:43020600-43021800	Weak transcription	Colonic Mucosa	Colon
37	chr10:43020600-43039200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:43020600-43047000	Weak transcription	HSMM	muscle
39	chr10:43020800-43021200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr10:43020800-43021400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr10:43020800-43023200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:43020800-43034200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr10:43021000-43022000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr10:43021000-43022800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr10:43021000-43023400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:43021000-43027000	Weak transcription	Aorta	Aorta
47	chr10:43021000-43027200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr10:43021000-43027200	Weak transcription	Ovary	ovary
49	chr10:43021000-43027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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