Variant report

Variant	rs3820312
Chromosome Location	chr1:180124450-180124451
allele	G/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180124065..180124574-chr1:180137270..180137775,2	MCF-7	breast:
2	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
3	chr1:180123935..180126561-chr1:180199070..180201304,3	MCF-7	breast:
4	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
5	chr1:180061211..180064450-chr1:180123630..180126274,3	MCF-7	breast:
6	chr1:180123681..180124534-chr16:66967758..66968260,2	Hela-S3	cervix:
7	chr1:179850220..179853546-chr1:180124207..180127412,4	MCF-7	breast:
8	chr1:180122867..180124515-chr12:122237701..122240027,2	MCF-7	breast:
9	chr1:180075321..180078076-chr1:180124133..180126626,2	K562	blood:
10	chr1:180067842..180070098-chr1:180124230..180125960,2	MCF-7	breast:
11	chr1:179922139..179925093-chr1:180123797..180126783,3	K562	blood:
12	chr1:180095863..180097872-chr1:180124437..180126586,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169905	Chromatin interaction
ENSG00000166595	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000121454	Chromatin interaction
ENSG00000212694	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10798738	0.82[LWK][hapmap];0.81[YRI][hapmap]
rs10913934	0.82[AMR][1000 genomes]
rs2298206	0.86[LWK][hapmap]
rs35481032	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753797	0.89[LWK][hapmap]
rs3753812	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767179	0.81[YRI][hapmap]
rs3767193	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767199	0.88[CEU][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs3820306	0.81[YRI][hapmap]
rs3820311	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3845392	0.93[ASN][1000 genomes]
rs6689602	0.82[LWK][hapmap]
rs7531169	0.95[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3820312	QSOX1	cis	Artery Tibial	GTEx
rs3820312	QSOX1	cis	lymphoblastoid	seeQTL
rs3820312	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	chr1:180122400-180124600	Active TSS	Esophagus	oesophagus
2	chr1:180122400-180125000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:180122800-180124800	Active TSS	Colon Smooth Muscle	Colon
4	chr1:180122800-180124800	Active TSS	Fetal Kidney	kidney
5	chr1:180122800-180125000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:180122800-180125200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:180122800-180125400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:180123000-180124600	Active TSS	Psoas Muscle	Psoas
9	chr1:180123000-180124800	Active TSS	Aorta	Aorta
10	chr1:180123000-180125000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:180123000-180125200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:180123000-180125600	Active TSS	Left Ventricle	heart
13	chr1:180123200-180124600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:180123200-180124600	Active TSS	Fetal Heart	heart
15	chr1:180123200-180124600	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:180123200-180124800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:180123200-180124800	Active TSS	HSMMtube	muscle
18	chr1:180123200-180125000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:180123200-180125200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr1:180123200-180125200	Active TSS	A549	lung
21	chr1:180123200-180125200	Active TSS	NHDF-Ad	bronchial
22	chr1:180123200-180125400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:180123200-180125400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:180123200-180125400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr1:180123200-180125400	Active TSS	Ovary	ovary
26	chr1:180123200-180125400	Active TSS	HSMM	muscle
27	chr1:180123200-180125600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:180123400-180124600	Active TSS	H1 Cell Line	embryonic stem cell
29	chr1:180123400-180124600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr1:180123400-180124600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr1:180123400-180124600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:180123400-180124600	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:180123400-180124600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:180123400-180124600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr1:180123400-180124600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr1:180123400-180124600	Active TSS	Brain Anterior Caudate	brain
37	chr1:180123400-180124600	Active TSS	Brain Cingulate Gyrus	brain
38	chr1:180123400-180124600	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr1:180123400-180124600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:180123400-180124600	Active TSS	Brain Substantia Nigra	brain
41	chr1:180123400-180124600	Active TSS	Right Ventricle	heart
42	chr1:180123400-180124600	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr1:180123400-180124600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:180123400-180124600	Active TSS	Thymus	Thymus
45	chr1:180123400-180124600	Active TSS	Spleen	Spleen
46	chr1:180123400-180124600	Active TSS	GM12878-XiMat	blood
47	chr1:180123400-180124600	Bivalent/Poised TSS	HepG2	liver
48	chr1:180123400-180124600	Active TSS	K562	blood
49	chr1:180123400-180124600	Active TSS	NH-A	brain
50	chr1:180123400-180124800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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