Variant report

Variant	rs12023795
Chromosome Location	chr1:85931390-85931391
allele	A/G
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	POLR2A	chr1:85929292-85931998	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:85929452-85931526	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:85928502-85932579	HUVEC	blood vessel:	n/a	n/a
4	POU2F2	chr1:85931262-85931543	GM12891	blood:	n/a	chr1:85931389-85931402
5	MYBL2	chr1:85930748-85931447	HepG2	liver:	n/a	n/a
6	REST	chr1:85929836-85931459	H1-neurons	neurons:	n/a	chr1:85930831-85930851 chr1:85931109-85931127
7	ZEB1	chr1:85929735-85931446	HepG2	liver:	n/a	chr1:85931200-85931212
8	MAX	chr1:85929823-85931420	A549	lung:	n/a	chr1:85930164-85930174
9	POLR2A	chr1:85930350-85931392	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:85929750-85931907	ProgFib	skin:	n/a	n/a
11	POLR2A	chr1:85928236-85932598	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr1:85929802-85931430	HCT-116	colon:	n/a	chr1:85930164-85930174
13	TAF1	chr1:85930070-85931394	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr1:85929890-85931414	ECC-1	luminal epithelium:	n/a	chr1:85930164-85930174
15	POLR2A	chr1:85928257-85932490	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr1:85928095-85932547	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:85928913-85932472	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:85929625-85931965	IMR90	lung:	n/a	n/a
19	MAZ	chr1:85929309-85931822	IMR90	lung:	n/a	chr1:85930164-85930174
20	POLR2A	chr1:85929268-85932094	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr1:85929989-85931559	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:85928110-85932105	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85744913..85746846-chr1:85930995..85932650,2	MCF-7	breast:
2	chr1:85929364..85932220-chr1:86042357..86044099,2	MCF-7	breast:
3	chr1:85931146..85932726-chr1:86032446..86035420,2	MCF-7	breast:
4	chr1:85927983..85931587-chr1:86046693..86050651,4	MCF-7	breast:
5	chr1:85930091..85932037-chr1:86045511..86048058,4	MCF-7	breast:
6	chr1:85929622..85931400-chr1:86044914..86046491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273264	TF binding region
DDAH1	TF binding region
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12021849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022443	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12022538	0.92[EUR][1000 genomes]
rs12024508	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12029684	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12033315	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12034206	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12034481	0.89[AMR][1000 genomes]
rs12038279	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12041140	0.89[AMR][1000 genomes]
rs12043604	0.84[EUR][1000 genomes]
rs12046433	0.89[AMR][1000 genomes]
rs12047139	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12049582	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1851782	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28847138	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs485987	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61164145	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv3437564	chr1:85929789-85932337	Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85928400-85931400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:85928400-85931600	Active TSS	Brain Anterior Caudate	brain
3	chr1:85928600-85931600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:85928800-85931400	Active TSS	Duodenum Mucosa	Duodenum
5	chr1:85929000-85931600	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:85929000-85931600	Active TSS	HSMM	muscle
7	chr1:85929000-85931600	Active TSS	HSMMtube	muscle
8	chr1:85929200-85931400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:85929200-85931400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:85929200-85931400	Active TSS	NHDF-Ad	bronchial
11	chr1:85929200-85931600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:85929200-85931600	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr1:85929200-85931800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:85929200-85931800	Active TSS	Brain Angular Gyrus	brain
15	chr1:85929400-85931400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85929600-85931400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
17	chr1:85929600-85931400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:85929600-85931400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:85929600-85931400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:85929600-85931400	Active TSS	Brain Substantia Nigra	brain
21	chr1:85929600-85931600	Active TSS	A549	lung
22	chr1:85929800-85931400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
23	chr1:85929800-85931400	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr1:85929800-85931400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:85929800-85931400	Active TSS	Colon Smooth Muscle	Colon
26	chr1:85929800-85931400	Active TSS	Fetal Kidney	kidney
27	chr1:85929800-85931800	Active TSS	Fetal Brain Female	brain
28	chr1:85930000-85931400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:85930000-85931400	Active TSS	HepG2	liver
30	chr1:85930000-85931600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr1:85930200-85931600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:85930200-85931800	Active TSS	Fetal Muscle Trunk	muscle
33	chr1:85930600-85931400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr1:85930600-85931600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:85930800-85931400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:85930800-85931400	Active TSS	Right Atrium	heart
37	chr1:85930800-85931600	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:85931000-85931400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
39	chr1:85931000-85931400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:85931000-85931400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr1:85931000-85931400	Flanking Active TSS	Fetal Lung	lung
42	chr1:85931000-85931400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr1:85931000-85931400	Flanking Active TSS	Placenta	Placenta
44	chr1:85931000-85931400	Flanking Active TSS	Ovary	ovary
45	chr1:85931000-85931400	Flanking Active TSS	Pancreas	Pancrea
46	chr1:85931000-85931400	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr1:85931000-85931400	Flanking Active TSS	Right Ventricle	heart
48	chr1:85931000-85931400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr1:85931000-85931400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:85931000-85931400	Flanking Active TSS	Stomach Smooth Muscle	stomach

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