Variant report

Variant	rs12378477
Chromosome Location	chr9:21396127-21396128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IFNA2-1	chr9:21394887-21396345	ENSG00000261696.1

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10965038	1.00[AFR][1000 genomes]
rs10965072	1.00[AFR][1000 genomes]
rs12378310	1.00[AFR][1000 genomes]
rs72703473	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892724	chr9:20690244-21517302	Genic enhancers Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
2	nsv892737	chr9:21352862-21408824	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2752289	chr9:21361957-21499624	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892738	chr9:21371264-21413085	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv466297	chr9:21391698-21507589	Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv613758	chr9:21391698-21507589	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21395600-21396600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:21395600-21396600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:21395800-21396200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr9:21395800-21396200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:21395800-21396200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr9:21395800-21396200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr9:21395800-21396200	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:21395800-21396200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
9	chr9:21395800-21396200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
10	chr9:21395800-21396200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:21395800-21396200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
12	chr9:21395800-21396200	Active TSS	Aorta	Aorta
13	chr9:21395800-21396200	Bivalent/Poised TSS	Colonic Mucosa	Colon
14	chr9:21395800-21396200	Active TSS	Pancreas	Pancrea
15	chr9:21395800-21396200	Active TSS	Psoas Muscle	Psoas
16	chr9:21395800-21396200	Active TSS	Right Atrium	heart
17	chr9:21395800-21396200	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
18	chr9:21395800-21396200	Active TSS	GM12878-XiMat	blood
19	chr9:21395800-21396400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr9:21395800-21396400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:21395800-21396400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:21395800-21396400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:21395800-21396400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:21395800-21396400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr9:21395800-21396400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
26	chr9:21395800-21396400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
27	chr9:21395800-21396400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:21395800-21396400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr9:21395800-21396400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
31	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
33	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
34	chr9:21395800-21396400	Flanking Active TSS	Primary hematopoietic stem cells	blood
35	chr9:21395800-21396400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:21395800-21396400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:21395800-21396400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Liver	Liver
40	chr9:21395800-21396400	Active TSS	Brain Angular Gyrus	brain
41	chr9:21395800-21396400	Active TSS	Brain Hippocampus Middle	brain
42	chr9:21395800-21396400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr9:21395800-21396400	Active TSS	Brain Substantia Nigra	brain
44	chr9:21395800-21396400	Active TSS	Colon Smooth Muscle	Colon
45	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
46	chr9:21395800-21396400	Bivalent/Poised TSS	Fetal Kidney	kidney
47	chr9:21395800-21396400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
48	chr9:21395800-21396400	Bivalent/Poised TSS	Fetal Lung	lung
49	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
50	chr9:21395800-21396400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach

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