Variant report

Variant	rs12044455
Chromosome Location	chr1:153915881-153915882
allele	C/T
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	chr1:153913791-153915938	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr1:153914086-153915919	K562	blood:	n/a	n/a
3	POLR2A	chr1:153915347-153915893	GM12892	blood:	n/a	n/a
4	POLR2A	chr1:153915140-153915888	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:153915072-153915940	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153915763..153918216-chr1:154155038..154156841,2	MCF-7	breast:

Variant related genes	Relation type
DENND4B	TF binding region
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11264522	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12023578	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12032520	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033532	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039936	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043354	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12045838	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12726350	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072704	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297895	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33998934	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34579266	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34665499	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35170146	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309017	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4323749	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61804837	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804838	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804839	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61805526	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427334	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527406	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9427246	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	nsv532552	chr1:153912047-153950752	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
8	esv3412635	chr1:153915772-153915913	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153896800-153917600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:153897000-153916400	Weak transcription	Fetal Brain Male	brain
3	chr1:153897400-153916600	Weak transcription	Fetal Heart	heart
4	chr1:153901000-153916400	Strong transcription	Fetal Thymus	thymus
5	chr1:153901400-153916400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:153901400-153916400	Strong transcription	Brain Germinal Matrix	brain
7	chr1:153901400-153916400	Strong transcription	Fetal Intestine Large	intestine
8	chr1:153901400-153916600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:153901400-153916600	Strong transcription	Fetal Stomach	stomach
10	chr1:153901400-153916800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:153901400-153916800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:153901400-153917200	Strong transcription	Fetal Intestine Small	intestine
13	chr1:153901600-153916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:153901600-153916200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:153901600-153916600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:153901600-153916600	Strong transcription	Thymus	Thymus
17	chr1:153901600-153916800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:153901600-153916800	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:153901600-153917000	Strong transcription	Fetal Brain Female	brain
20	chr1:153901800-153916400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:153901800-153917000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:153902000-153916400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:153902000-153916600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:153902000-153916600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:153902000-153916600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr1:153902000-153917000	Strong transcription	NHLF	lung
27	chr1:153902200-153916600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:153902400-153916400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:153902400-153916400	Strong transcription	Dnd41	blood
30	chr1:153902400-153916600	Strong transcription	Ovary	ovary
31	chr1:153902400-153916800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:153902600-153916600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:153902800-153916400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:153902800-153916600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:153902800-153916600	Strong transcription	A549	lung
36	chr1:153903000-153917000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:153903800-153916000	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:153904600-153916400	Strong transcription	Brain Angular Gyrus	brain
39	chr1:153904800-153916000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:153904800-153917000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:153905000-153917400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:153906800-153916400	Weak transcription	Right Atrium	heart
43	chr1:153908000-153917000	Strong transcription	K562	blood
44	chr1:153909200-153918000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:153910200-153917400	Weak transcription	HUVEC	blood vessel
46	chr1:153910400-153917000	Weak transcription	Stomach Mucosa	stomach
47	chr1:153910400-153917400	Weak transcription	NH-A	brain
48	chr1:153910400-153917400	Weak transcription	NHDF-Ad	bronchial
49	chr1:153910400-153917600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:153910400-153918000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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