Variant report

Variant	rs1758143
Chromosome Location	chr1:179849852-179849853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179848947-179849877	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr1:179849721-179849891	GM12878	blood:	n/a	chr1:179849750-179849764
3	ARID3A	chr1:179849058-179849997	K562	blood:	n/a	chr1:179849295-179849311

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:
2	chr1:179833317..179835863-chr1:179849395..179853272,4	MCF-7	breast:
3	chr1:179849806..179852481-chr17:56735365..56738310,2	MCF-7	breast:
4	chr1:179849600..179851970-chr1:180040830..180043217,3	K562	blood:
5	chr1:179848758..179850478-chr1:179862468..179865015,2	MCF-7	breast:
6	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
7	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
8	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
9	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

No data

Variant related genes	Relation type
TOR1AIP2	TF binding region
TOR1AIP1	TF binding region
ENSG00000258664	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000116260	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1148813	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1148814	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1148816	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281409	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281414	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1281415	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1281419	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1281425	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1281431	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1290274	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1295972	0.94[EUR][1000 genomes]
rs1299683	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1299685	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17370666	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2762857	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2777907	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2777916	0.89[EUR][1000 genomes]
rs2794584	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs476280	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs524166	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555755	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs576723	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs651455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs668813	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683812	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS 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 target site	48 gene(s)	inside rSNPs	diseases
7	nsv518936	chr1:179847402-179858333	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	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	chr1:179847000-179850800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:179847200-179850400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:179847200-179850600	Weak transcription	Fetal Thymus	thymus
4	chr1:179847200-179850800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:179847200-179851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:179847200-179851000	Weak transcription	Gastric	stomach
7	chr1:179847200-179851000	Weak transcription	Lung	lung
8	chr1:179847400-179850200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:179847400-179850200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:179847400-179850200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:179847400-179850200	Weak transcription	HMEC	breast
12	chr1:179847400-179850200	Weak transcription	NHEK	skin
13	chr1:179847400-179850200	Weak transcription	Osteobl	bone
14	chr1:179847400-179850400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:179847400-179850400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:179847400-179850400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:179847400-179850400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:179847400-179850400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:179847400-179850400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:179847400-179850400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:179847400-179850400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:179847400-179850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:179847400-179850400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:179847400-179850400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:179847400-179850400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:179847400-179850400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:179847400-179850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:179847400-179850400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:179847400-179850400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:179847400-179850400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:179847400-179850400	Weak transcription	Adipose Nuclei	Adipose
32	chr1:179847400-179850400	Enhancers	Liver	Liver
33	chr1:179847400-179850400	Weak transcription	Brain Angular Gyrus	brain
34	chr1:179847400-179850400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:179847400-179850400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:179847400-179850400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:179847400-179850400	Weak transcription	Fetal Brain Male	brain
38	chr1:179847400-179850400	Weak transcription	Fetal Kidney	kidney
39	chr1:179847400-179850400	Weak transcription	Fetal Lung	lung
40	chr1:179847400-179850400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:179847400-179850400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:179847400-179850400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:179847400-179850400	Weak transcription	Right Atrium	heart
44	chr1:179847400-179850400	Weak transcription	Right Ventricle	heart
45	chr1:179847400-179850400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:179847400-179850400	Weak transcription	HSMM	muscle
47	chr1:179847400-179850400	Weak transcription	HUVEC	blood vessel
48	chr1:179847400-179850400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr1:179847400-179850400	Weak transcription	NH-A	brain
50	chr1:179847400-179850400	Weak transcription	NHDF-Ad	bronchial

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