Variant report

Variant	rs1255400
Chromosome Location	chr10:42971925-42971926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr10:42969491-42973054	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:42969989..42972327-chr10:43278200..43280239,2	K562	blood:

Variant related genes	Relation type
CCNYL2	TF binding region
ENSG00000165733	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1255412	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1760687	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2801951	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv550669	chr10:42725663-42982645	ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv471665	chr10:42852460-43006666	Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1051346	chr10:42864101-43006803	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	nsv947882	chr10:42970371-42973594	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1255400	LINC00839	cis	Esophagus Muscularis	GTEx
rs1255400	LINC00839	cis	Artery Tibial	GTEx
rs1255400	LINC00839	cis	Esophagus Mucosa	GTEx
rs1255400	CCNYL2	cis	Artery Aorta	GTEx
rs1255400	LINC00839	cis	Skin Sun Exposed Lower leg	GTEx
rs1255400	LINC00839	cis	Artery Aorta	GTEx
rs1255400	LINC00839	cis	lung	GTEx
rs1255400	LINC00839	cis	Thyroid	GTEx
rs1255400	LINC00839	cis	Nerve Tibial	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:42970600-42972000	Active TSS	Brain Cingulate Gyrus	brain
2	chr10:42970600-42972600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:42970800-42972000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:42970800-42972000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
5	chr10:42970800-42972000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:42970800-42972000	Active TSS	Brain Angular Gyrus	brain
7	chr10:42970800-42972000	Active TSS	Brain Anterior Caudate	brain
8	chr10:42970800-42972000	ZNF genes & repeats	Fetal Stomach	stomach
9	chr10:42970800-42972200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr10:42970800-42972200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:42970800-42972200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:42970800-42972200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr10:42970800-42972200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr10:42970800-42972600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:42970800-42972600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr10:42971000-42972000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
17	chr10:42971000-42972000	ZNF genes & repeats	Aorta	Aorta
18	chr10:42971000-42972000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr10:42971000-42972000	Active TSS	Colonic Mucosa	Colon
20	chr10:42971000-42972000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
21	chr10:42971000-42972000	Active TSS	Spleen	Spleen
22	chr10:42971000-42972000	Bivalent/Poised TSS	HepG2	liver
23	chr10:42971000-42972000	Active TSS	K562	blood
24	chr10:42971000-42972000	Active TSS	NH-A	brain
25	chr10:42971000-42972000	Active TSS	NHLF	lung
26	chr10:42971000-42972200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr10:42971000-42972200	Active TSS	Ovary	ovary
28	chr10:42971000-42972200	Active TSS	Osteobl	bone
29	chr10:42971000-42972400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr10:42971000-42972400	Active TSS	HUVEC	blood vessel
31	chr10:42971200-42972000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:42971200-42972000	Active TSS	Esophagus	oesophagus
33	chr10:42971200-42972000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr10:42971200-42972800	Active TSS	HMEC	breast
35	chr10:42971400-42972000	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr10:42971400-42972000	Flanking Active TSS	Lung	lung
37	chr10:42971400-42973000	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr10:42971800-42972000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr10:42971800-42972000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr10:42971800-42972000	Enhancers	Pancreas	Pancrea
41	chr10:42971800-42972400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr10:42971800-42972600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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