Variant report

Variant	rs12079856
Chromosome Location	chr1:169073002-169073003
allele	A/C
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	NR3C1	chr1:169072712-169073179	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
2	GATA2	chr1:169072661-169073603	SH-SY5Y	brain:	n/a	n/a
3	NR3C1	chr1:169072733-169073156	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
4	NR3C1	chr1:169072718-169073072	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
5	SMARCB1	chr1:169071730-169073071	Hela-S3	cervix:	n/a	chr1:169071978-169071987 chr1:169071979-169071988
6	NR3C1	chr1:169072755-169073151	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
7	NR3C1	chr1:169072666-169073208	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
8	NR3C1	chr1:169072655-169073277	A549	lung:	n/a	chr1:169072885-169072901 chr1:169072886-169072900 chr1:169073019-169073033 chr1:169072885-169072901
9	POLR2A	chr1:169072998-169073061	HepG2	liver:	n/a	n/a
10	ESRRA	chr1:169071901-169073461	GM12878	blood:	n/a	chr1:169073087-169073103 chr1:169073094-169073104 chr1:169073087-169073103 chr1:169072995-169073005 chr1:169073094-169073104 chr1:169073092-169073108 chr1:169072990-169073004 chr1:169072989-169073005 chr1:169072995-169073004 chr1:169072990-169073009 chr1:169073092-169073104 chr1:169072171-169072184

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169071736..169074539-chr1:169075134..169076733,2	K562	blood:
2	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:

Variant related genes	Relation type
ATP1B1	TF binding region
ENSG00000237707	TF binding region
ENSG00000203601	Chromatin interaction
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12061601	0.98[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12751593	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1320976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320977	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534984	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892092	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892093	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362572	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28362573	0.93[ASN][1000 genomes]
rs4656647	0.88[EUR][1000 genomes]
rs59732929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672876	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169068000-169074600	Enhancers	Fetal Heart	heart
2	chr1:169068800-169074600	Enhancers	Fetal Intestine Large	intestine
3	chr1:169068800-169074600	Enhancers	Fetal Intestine Small	intestine
4	chr1:169069200-169074400	Enhancers	HepG2	liver
5	chr1:169070000-169073800	Weak transcription	Gastric	stomach
6	chr1:169070600-169074400	Enhancers	A549	lung
7	chr1:169070600-169074600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:169070800-169074200	Weak transcription	Liver	Liver
9	chr1:169071000-169074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:169071200-169073600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:169071400-169073600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:169071600-169073200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:169071600-169073200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:169071600-169073200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:169071600-169073200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr1:169071600-169074400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr1:169071600-169074400	Enhancers	Stomach Mucosa	stomach
18	chr1:169071600-169074600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:169071800-169073800	Enhancers	Spleen	Spleen
20	chr1:169072000-169074400	Weak transcription	Adipose Nuclei	Adipose
21	chr1:169072000-169074400	Weak transcription	Fetal Lung	lung
22	chr1:169072200-169073200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:169072200-169073200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:169072200-169073400	Weak transcription	Small Intestine	intestine
25	chr1:169072200-169074800	Weak transcription	Right Atrium	heart
26	chr1:169072400-169073200	Enhancers	Brain Cingulate Gyrus	brain
27	chr1:169072400-169074400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:169072400-169074600	Weak transcription	Fetal Brain Female	brain
29	chr1:169072400-169075000	Weak transcription	Aorta	Aorta
30	chr1:169072600-169073200	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr1:169072600-169073200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:169072600-169074400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:169072600-169074400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr1:169072600-169074600	Enhancers	Pancreas	Pancrea
35	chr1:169072600-169074800	Enhancers	Brain Substantia Nigra	brain
36	chr1:169072800-169073200	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr1:169072800-169073400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr1:169072800-169073400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:169072800-169073800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:169072800-169074000	Weak transcription	Brain Germinal Matrix	brain
41	chr1:169072800-169074000	Weak transcription	Fetal Brain Male	brain
42	chr1:169072800-169074400	Enhancers	Brain Hippocampus Middle	brain
43	chr1:169072800-169074400	Enhancers	Colonic Mucosa	Colon
44	chr1:169072800-169074400	Enhancers	Fetal Kidney	kidney
45	chr1:169072800-169074400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:169072800-169074600	Weak transcription	Colon Smooth Muscle	Colon
47	chr1:169072800-169074800	Enhancers	Esophagus	oesophagus
48	chr1:169073000-169073200	Enhancers	Brain Anterior Caudate	brain
49	chr1:169073000-169073200	Enhancers	Ovary	ovary
50	chr1:169073000-169073600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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