Variant report

Variant	rs12084253
Chromosome Location	chr1:85720326-85720327
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:85689720..85692131-chr1:85719135..85721500,2	MCF-7	breast:
2	chr1:85687931..85689512-chr1:85720221..85722381,2	MCF-7	breast:
3	chr1:85574817..85576177-chr1:85720143..85721098,6	K562	blood:
4	chr1:85719208..85720830-chr1:85723988..85725529,2	MCF-7	breast:
5	chr1:85410252..85411181-chr1:85719873..85720677,4	K562	blood:
6	chr1:85665862..85668406-chr1:85717337..85721065,4	MCF-7	breast:
7	chr1:85575122..85575745-chr1:85720198..85721084,2	MCF-7	breast:
8	chr1:85410353..85411305-chr1:85719958..85721105,6	MCF-7	breast:
9	chr1:85719208..85720970-chr1:85755325..85757545,2	K562	blood:
10	chr1:85410258..85411298-chr1:85720149..85720894,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1077996	0.81[AFR][1000 genomes]
rs11161573	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11576939	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11580090	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12061512	0.91[ASN][1000 genomes]
rs12403960	0.93[ASN][1000 genomes]
rs12405767	0.85[ASN][1000 genomes]
rs4949927	0.91[ASN][1000 genomes]
rs4949928	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55808228	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60325409	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85707000-85721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:85707000-85722800	Weak transcription	HepG2	liver
3	chr1:85707000-85723000	Weak transcription	Stomach Mucosa	stomach
4	chr1:85707800-85724400	Weak transcription	Lung	lung
5	chr1:85709800-85724200	Weak transcription	Colonic Mucosa	Colon
6	chr1:85710400-85721400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:85710400-85724000	Weak transcription	Ovary	ovary
8	chr1:85710400-85724000	Weak transcription	Right Ventricle	heart
9	chr1:85710600-85722600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:85710600-85723800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:85710800-85724000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:85710800-85724200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:85710800-85724400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:85710800-85724600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:85711600-85723800	Weak transcription	HSMMtube	muscle
16	chr1:85712000-85723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:85712000-85723000	Weak transcription	NHLF	lung
18	chr1:85712200-85722800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:85712200-85724000	Weak transcription	Fetal Stomach	stomach
20	chr1:85713000-85722800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:85713200-85724000	Weak transcription	Thymus	Thymus
22	chr1:85714400-85721400	Weak transcription	Brain Anterior Caudate	brain
23	chr1:85714600-85724200	Weak transcription	Gastric	stomach
24	chr1:85714800-85720400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:85714800-85723400	Weak transcription	Fetal Brain Male	brain
26	chr1:85715000-85721200	Weak transcription	Fetal Intestine Small	intestine
27	chr1:85715000-85722600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:85715000-85724200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:85715200-85721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:85715200-85724200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:85715800-85723000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:85715800-85723000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:85716000-85723400	Weak transcription	Spleen	Spleen
34	chr1:85716200-85723200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:85716200-85723600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr1:85716200-85723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:85716400-85722600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:85716400-85723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:85716600-85722600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:85716600-85723600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:85716800-85723000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:85716800-85723400	Strong transcription	Fetal Thymus	thymus
43	chr1:85716800-85723800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:85716800-85723800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr1:85717000-85722600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr1:85717000-85723400	Strong transcription	NHDF-Ad	bronchial
47	chr1:85717000-85723800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:85717200-85722800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:85717600-85723400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:85717800-85721600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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