Variant report

Variant	rs12366401
Chromosome Location	chr12:42326174-42326175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GXYLT1-1	chr12:42325924-42326394	ENSG00000257239.1

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10491998	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10735999	0.97[ASN][1000 genomes]
rs10785314	1.00[ASN][1000 genomes]
rs1234016	1.00[ASN][1000 genomes]
rs1234024	1.00[ASN][1000 genomes]
rs1497168	0.94[ASN][1000 genomes]
rs2109531	0.97[ASN][1000 genomes]
rs4326861	0.96[ASN][1000 genomes]
rs4768384	1.00[ASN][1000 genomes]
rs7309345	0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised 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	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42323600-42327000	Active TSS	Right Atrium	heart
2	chr12:42324400-42326600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
3	chr12:42324400-42326800	Active TSS	Aorta	Aorta
4	chr12:42324400-42327000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:42324600-42326600	Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr12:42324600-42327000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:42324600-42327000	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr12:42324800-42327000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr12:42325000-42326600	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr12:42325200-42326200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:42325200-42326200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:42325200-42326200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:42325200-42326200	Weak transcription	Stomach Mucosa	stomach
14	chr12:42325200-42326200	Weak transcription	NHDF-Ad	bronchial
15	chr12:42325200-42326200	Weak transcription	NHEK	skin
16	chr12:42325200-42326400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr12:42325200-42327000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:42325200-42327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:42325400-42326200	Enhancers	Gastric	stomach
20	chr12:42325400-42326200	Weak transcription	NHLF	lung
21	chr12:42325800-42326200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:42325800-42326800	Active TSS	Left Ventricle	heart
23	chr12:42325800-42327000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:42325800-42327000	Active TSS	Brain Anterior Caudate	brain
25	chr12:42325800-42327000	Active TSS	Brain Hippocampus Middle	brain
26	chr12:42325800-42327000	Active TSS	Brain Substantia Nigra	brain
27	chr12:42326000-42326200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:42326000-42326200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:42326000-42326200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:42326000-42326200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:42326000-42326200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:42326000-42326200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:42326000-42326200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:42326000-42326200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:42326000-42326200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:42326000-42326200	Active TSS	Adipose Nuclei	Adipose
37	chr12:42326000-42326200	Active TSS	Brain Germinal Matrix	brain
38	chr12:42326000-42326200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:42326000-42326200	Enhancers	Colonic Mucosa	Colon
40	chr12:42326000-42326200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr12:42326000-42326200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr12:42326000-42326200	Enhancers	Fetal Brain Male	brain
43	chr12:42326000-42326200	Flanking Active TSS	Fetal Lung	lung
44	chr12:42326000-42326200	Flanking Active TSS	Fetal Muscle Trunk	muscle
45	chr12:42326000-42326200	Active TSS	NH-A	brain
46	chr12:42326000-42326200	Enhancers	Osteobl	bone
47	chr12:42326000-42326400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:42326000-42326400	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr12:42326000-42326400	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr12:42326000-42326400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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