Variant report

Variant	rs3767199
Chromosome Location	chr1:180124667-180124668
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
2	chr1:180123935..180126561-chr1:180199070..180201304,3	MCF-7	breast:
3	chr1:180112122..180113810-chr1:180124529..180126032,2	MCF-7	breast:
4	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
5	chr1:180051158..180053588-chr1:180124507..180126558,2	K562	blood:
6	chr1:180061211..180064450-chr1:180123630..180126274,3	MCF-7	breast:
7	chr1:179850220..179853546-chr1:180124207..180127412,4	MCF-7	breast:
8	chr1:180075321..180078076-chr1:180124133..180126626,2	K562	blood:
9	chr1:180067842..180070098-chr1:180124230..180125960,2	MCF-7	breast:
10	chr1:179922139..179925093-chr1:180123797..180126783,3	K562	blood:
11	chr1:180095863..180097872-chr1:180124437..180126586,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000121454	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10157671	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs12060240	0.90[JPT][hapmap]
rs12064324	0.90[JPT][hapmap]
rs12079539	0.81[JPT][hapmap]
rs35481032	0.90[EUR][1000 genomes]
rs3753811	0.90[JPT][hapmap]
rs3753812	0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs3767190	0.90[JPT][hapmap]
rs3767193	0.91[EUR][1000 genomes]
rs3767196	0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes]
rs3767197	0.90[JPT][hapmap]
rs3820311	0.91[EUR][1000 genomes]
rs3820312	0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3355160	chr1:180122754-180125702	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3767199	QSOX1	cis	Artery Tibial	GTEx
rs3767199	QSOX1	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180122400-180125000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180122800-180124800	Active TSS	Colon Smooth Muscle	Colon
3	chr1:180122800-180124800	Active TSS	Fetal Kidney	kidney
4	chr1:180122800-180125000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:180122800-180125200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:180122800-180125400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:180123000-180124800	Active TSS	Aorta	Aorta
8	chr1:180123000-180125000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:180123000-180125200	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:180123000-180125600	Active TSS	Left Ventricle	heart
11	chr1:180123200-180124800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:180123200-180124800	Active TSS	HSMMtube	muscle
13	chr1:180123200-180125000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:180123200-180125200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr1:180123200-180125200	Active TSS	A549	lung
16	chr1:180123200-180125200	Active TSS	NHDF-Ad	bronchial
17	chr1:180123200-180125400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:180123200-180125400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:180123200-180125400	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:180123200-180125400	Active TSS	Ovary	ovary
21	chr1:180123200-180125400	Active TSS	HSMM	muscle
22	chr1:180123200-180125600	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:180123400-180124800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:180123400-180124800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr1:180123400-180124800	Active TSS	Brain Hippocampus Middle	brain
26	chr1:180123400-180124800	Active TSS	Fetal Stomach	stomach
27	chr1:180123400-180124800	Active TSS	Small Intestine	intestine
28	chr1:180123400-180124800	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:180123400-180125000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:180123400-180125000	Active TSS	Brain Angular Gyrus	brain
31	chr1:180123400-180125200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:180123400-180125200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:180123400-180125200	Active TSS	Fetal Lung	lung
34	chr1:180123400-180125200	Active TSS	Gastric	stomach
35	chr1:180123400-180125200	Active TSS	Osteobl	bone
36	chr1:180123400-180125400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:180123400-180125400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:180123400-180125600	Active TSS	Stomach Mucosa	stomach
39	chr1:180123600-180124800	Active TSS	Muscle Satellite Cultured Cells	--
40	chr1:180123600-180124800	Active TSS	Placenta Amnion	Placenta Amnion
41	chr1:180123600-180124800	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:180123600-180125400	Active TSS	Fetal Brain Male	brain
43	chr1:180123600-180125600	Active TSS	NHLF	lung
44	chr1:180124000-180126000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:180124200-180125000	Flanking Active TSS	Primary B cells from cord blood	blood
46	chr1:180124200-180125600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:180124400-180124800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:180124400-180124800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:180124400-180124800	Flanking Active TSS	Liver	Liver
50	chr1:180124400-180124800	Bivalent/Poised TSS	Fetal Brain Female	brain

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