Variant report

Variant	rs1053166
Chromosome Location	chr1:185088697-185088698
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:185087227..185089140-chr1:185125216..185126915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116668	Chromatin interaction
ENSG00000121486	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10737256	0.82[TSI][hapmap]
rs10911679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12063375	0.84[AMR][1000 genomes]
rs12119759	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12385701	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12563135	0.82[ASN][1000 genomes]
rs12566404	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1322646	0.82[TSI][hapmap]
rs1407557	0.82[TSI][hapmap]
rs2146329	0.82[TSI][hapmap]
rs2378957	0.90[GIH][hapmap]
rs28609768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs34916432	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34969721	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35507672	0.81[AMR][1000 genomes]
rs6674490	0.84[TSI][hapmap]
rs6677056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs6684586	0.81[TSI][hapmap]
rs6699626	0.93[EUR][1000 genomes]
rs7523448	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7548237	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs950327	1.00[CEU][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv548396	chr1:185038104-185151378	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv521613	chr1:185071831-185171869	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv872588	chr1:185081903-185117688	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1053166	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
2	chr1:185054400-185101800	Weak transcription	A549	lung
3	chr1:185055400-185096200	Weak transcription	Hela-S3	cervix
4	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:185057600-185094600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:185058600-185089000	Weak transcription	Ovary	ovary
7	chr1:185058800-185093600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:185067800-185095400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:185068400-185110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:185069400-185091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:185070000-185101400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:185070200-185088800	Weak transcription	HSMM	muscle
14	chr1:185070400-185089200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:185073600-185092800	Weak transcription	Fetal Kidney	kidney
16	chr1:185073600-185115000	Weak transcription	NH-A	brain
17	chr1:185078800-185088800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:185078800-185102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:185079800-185102000	Weak transcription	Small Intestine	intestine
20	chr1:185080000-185101000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:185081200-185091400	Weak transcription	GM12878-XiMat	blood
22	chr1:185081600-185091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:185081800-185088800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:185081800-185092800	Weak transcription	HUVEC	blood vessel
25	chr1:185082000-185092800	Weak transcription	K562	blood
26	chr1:185082200-185095200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:185082400-185088800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:185082400-185093600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:185082600-185100400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:185082600-185101400	Weak transcription	Esophagus	oesophagus
31	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
32	chr1:185083400-185093400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:185084000-185089200	Weak transcription	Left Ventricle	heart
34	chr1:185084200-185089000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:185084200-185103400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
37	chr1:185084400-185091000	Weak transcription	Brain Angular Gyrus	brain
38	chr1:185084400-185093000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:185084600-185089000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:185084600-185089000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:185084600-185102400	Weak transcription	Aorta	Aorta
42	chr1:185084600-185104200	Weak transcription	Pancreas	Pancrea
43	chr1:185084800-185088800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:185084800-185089000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:185084800-185091800	Weak transcription	Fetal Intestine Small	intestine
46	chr1:185085000-185121400	Weak transcription	NHEK	skin
47	chr1:185085400-185090400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:185085600-185091000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:185085600-185094400	Weak transcription	Lung	lung

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