Variant report

Variant	rs17279594
Chromosome Location	chr1:179849356-179849357
allele	A/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	chr1:179848947-179849877	MCF10A-Er-Src	breast:	n/a	n/a
2	ARID3A	chr1:179849058-179849997	K562	blood:	n/a	chr1:179849295-179849311

No.	Distal block	Cell Line	Cell type
1	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:
2	chr1:179848758..179850478-chr1:179862468..179865015,2	MCF-7	breast:
3	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
4	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
5	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:

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

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10913901	0.94[ASN][1000 genomes]
rs10913906	0.92[ASN][1000 genomes]
rs11546310	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17370777	1.00[YRI][hapmap]
rs17370826	1.00[YRI][hapmap]
rs2318388	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753398	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4310406	0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4651052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55706288	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58392320	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61184002	0.98[ASN][1000 genomes]
rs6657364	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6666510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680290	0.94[ASN][1000 genomes]
rs6689160	1.00[YRI][hapmap]
rs7411457	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530362	1.00[JPT][hapmap];0.89[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:118 , 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	chr1:179847200-179849800	Weak transcription	HSMMtube	muscle
3	chr1:179847200-179850400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:179847200-179850600	Weak transcription	Fetal Thymus	thymus
5	chr1:179847200-179850800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:179847200-179851000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:179847200-179851000	Weak transcription	Gastric	stomach
8	chr1:179847200-179851000	Weak transcription	Lung	lung
9	chr1:179847400-179849600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:179847400-179849800	Weak transcription	Primary T cells from cord blood	blood
11	chr1:179847400-179849800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:179847400-179849800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:179847400-179849800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:179847400-179849800	Weak transcription	Fetal Intestine Large	intestine
15	chr1:179847400-179850200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:179847400-179850200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:179847400-179850200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:179847400-179850200	Weak transcription	HMEC	breast
19	chr1:179847400-179850200	Weak transcription	NHEK	skin
20	chr1:179847400-179850200	Weak transcription	Osteobl	bone
21	chr1:179847400-179850400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:179847400-179850400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:179847400-179850400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:179847400-179850400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:179847400-179850400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:179847400-179850400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:179847400-179850400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:179847400-179850400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:179847400-179850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:179847400-179850400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:179847400-179850400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:179847400-179850400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:179847400-179850400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:179847400-179850400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:179847400-179850400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr1:179847400-179850400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:179847400-179850400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:179847400-179850400	Weak transcription	Adipose Nuclei	Adipose
39	chr1:179847400-179850400	Enhancers	Liver	Liver
40	chr1:179847400-179850400	Weak transcription	Brain Angular Gyrus	brain
41	chr1:179847400-179850400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:179847400-179850400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:179847400-179850400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:179847400-179850400	Weak transcription	Fetal Brain Male	brain
45	chr1:179847400-179850400	Weak transcription	Fetal Kidney	kidney
46	chr1:179847400-179850400	Weak transcription	Fetal Lung	lung
47	chr1:179847400-179850400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:179847400-179850400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:179847400-179850400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:179847400-179850400	Weak transcription	Right Atrium	heart

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