Variant report

Variant	rs6686428
Chromosome Location	chr1:180125753-180125754
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180094856..180097003-chr1:180124933..180127557,2	K562	blood:
2	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
3	chr1:180123935..180126561-chr1:180199070..180201304,3	MCF-7	breast:
4	chr1:180112122..180113810-chr1:180124529..180126032,2	MCF-7	breast:
5	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
6	chr1:180051158..180053588-chr1:180124507..180126558,2	K562	blood:
7	chr1:180061211..180064450-chr1:180123630..180126274,3	MCF-7	breast:
8	chr1:180094624..180096269-chr1:180125316..180126971,2	MCF-7	breast:
9	chr1:179845447..179846955-chr1:180125305..180127512,2	K562	blood:
10	chr1:179850220..179853546-chr1:180124207..180127412,4	MCF-7	breast:
11	chr1:180075321..180078076-chr1:180124133..180126626,2	K562	blood:
12	chr1:180067842..180070098-chr1:180124230..180125960,2	MCF-7	breast:
13	chr1:180039217..180042128-chr1:180125172..180126963,2	K562	blood:
14	chr1:179922139..179925093-chr1:180123797..180126783,3	K562	blood:
15	chr1:180095863..180097872-chr1:180124437..180126586,3	MCF-7	breast:

No data

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

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12741050	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60022752	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664185	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541022	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1011933	chr1:180125666-180171361	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6686428	QSOX1	cis	Artery Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180124000-180126000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:180124400-180126800	Flanking Active TSS	Duodenum Mucosa	Duodenum
3	chr1:180124600-180125800	Flanking Active TSS	HUVEC	blood vessel
4	chr1:180124600-180126000	Flanking Active TSS	Brain Cingulate Gyrus	brain
5	chr1:180124600-180126200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:180124600-180126200	Flanking Active TSS	K562	blood
7	chr1:180124600-180126400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:180124600-180126600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:180124600-180126600	Flanking Active TSS	NHEK	skin
10	chr1:180124600-180126800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr1:180124600-180127200	Flanking Active TSS	NH-A	brain
12	chr1:180124600-180129400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:180124800-180125800	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr1:180124800-180125800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr1:180124800-180126000	Flanking Active TSS	Fetal Stomach	stomach
16	chr1:180124800-180126800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr1:180124800-180127000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:180124800-180127000	Enhancers	Spleen	Spleen
19	chr1:180124800-180128000	Enhancers	Liver	Liver
20	chr1:180124800-180151000	Weak transcription	Aorta	Aorta
21	chr1:180125000-180125800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:180125000-180125800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:180125000-180125800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:180125000-180125800	Active TSS	Right Atrium	heart
25	chr1:180125000-180126000	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:180125000-180126000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:180125000-180126000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr1:180125000-180126000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:180125000-180126200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:180125000-180126200	Weak transcription	Small Intestine	intestine
31	chr1:180125000-180126600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:180125000-180126800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:180125000-180126800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:180125000-180126800	Flanking Active TSS	Fetal Brain Female	brain
35	chr1:180125000-180126800	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:180125000-180127200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:180125000-180127400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:180125000-180127400	Active TSS	Esophagus	oesophagus
39	chr1:180125000-180127600	Enhancers	Fetal Heart	heart
40	chr1:180125000-180127600	Active TSS	Rectal Smooth Muscle	rectum
41	chr1:180125000-180128400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr1:180125000-180129400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:180125000-180133200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:180125000-180136000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:180125200-180125800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:180125200-180125800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:180125200-180125800	Enhancers	Primary T cells from cord blood	blood
48	chr1:180125200-180125800	Enhancers	Colon Smooth Muscle	Colon
49	chr1:180125200-180126000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:180125200-180126000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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