Variant report

Variant	rs12059074
Chromosome Location	chr1:84542214-84542215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:84541895-84545296	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:84542201-84544432	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:84463410..84466364-chr1:84542152..84546505,5	K562	blood:
2	chr1:84387778..84389882-chr1:84541236..84543359,2	K562	blood:
3	chr1:84540590..84543508-chr1:84558962..84560991,2	K562	blood:
4	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:
5	chr1:84540791..84543154-chr1:84633401..84635166,2	K562	blood:
6	chr1:84541371..84543109-chr1:84583953..84586517,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTLL7-3	chr1:84542062-84543325	XLOC_000889
2	lnc-TTLL7-3	chr1:84542014-84543614	ENSG00000271576.1
3	lnc-TTLL7-3	chr1:84542014-84543655	NONHSAT004184

No data

Variant related genes	Relation type
PRKACB	TF binding region
ENSG00000213540	Chromatin interaction
ENSG00000137941	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11163896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062467	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064346	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069372	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075911	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84536600-84542400	Weak transcription	Fetal Lung	lung
2	chr1:84538400-84542400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:84538400-84542800	Weak transcription	HSMM	muscle
4	chr1:84538600-84542400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr1:84538600-84542400	Weak transcription	Osteobl	bone
6	chr1:84539200-84542400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:84540200-84542400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:84541000-84542400	Enhancers	HepG2	liver
9	chr1:84541200-84542400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:84541200-84542400	Enhancers	Brain Hippocampus Middle	brain
11	chr1:84541200-84542400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:84541200-84542400	Enhancers	Dnd41	blood
13	chr1:84541400-84542400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:84541400-84542400	Weak transcription	Brain Anterior Caudate	brain
15	chr1:84541400-84542600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:84542000-84542400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:84542000-84542400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:84542000-84542400	Enhancers	A549	lung
19	chr1:84542000-84542400	Enhancers	GM12878-XiMat	blood
20	chr1:84542000-84542800	Enhancers	Liver	Liver
21	chr1:84542000-84544600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr1:84542000-84544800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:84542000-84545200	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:84542200-84542400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:84542200-84542400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:84542200-84542400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:84542200-84542400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:84542200-84542400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:84542200-84542400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:84542200-84542400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:84542200-84542400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:84542200-84542400	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:84542200-84542400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:84542200-84542400	Enhancers	Fetal Brain Male	brain
35	chr1:84542200-84542400	Enhancers	Fetal Heart	heart
36	chr1:84542200-84542400	Enhancers	Stomach Smooth Muscle	stomach
37	chr1:84542200-84542400	Enhancers	HSMMtube	muscle
38	chr1:84542200-84542400	Active TSS	K562	blood
39	chr1:84542200-84542600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:84542200-84542800	Enhancers	Brain Angular Gyrus	brain
41	chr1:84542200-84542800	Enhancers	Rectal Smooth Muscle	rectum
42	chr1:84542200-84542800	Flanking Active TSS	Hela-S3	cervix
43	chr1:84542200-84543000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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