Variant report

Variant	rs7548237
Chromosome Location	chr1:185128250-185128251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:185127838-185128387	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:185124212..185128355-chr1:185283797..185287901,7	K562	blood:
2	chr1:184721859..184724654-chr1:185126581..185128573,2	MCF-7	breast:
3	chr1:184683246..184684894-chr1:185126908..185129341,2	K562	blood:
4	chr1:184941281..184944338-chr1:185124829..185129491,4	K562	blood:
5	chr1:185123673..185127024-chr1:185127096..185129642,5	MCF-7	breast:
6	chr1:185013031..185014942-chr1:185128013..185130394,2	K562	blood:
7	chr1:185124896..185128464-chr1:185139300..185142346,3	MCF-7	breast:

No data

Variant related genes	Relation type
TRMT1L	TF binding region
ENSG00000121481	Chromatin interaction
ENSG00000273004	Chromatin interaction
ENSG00000231084	Chromatin interaction
ENSG00000116668	Chromatin interaction
ENSG00000135842	Chromatin interaction
ENSG00000121486	Chromatin interaction
ENSG00000116679	Chromatin interaction
ENSG00000116406	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1053166	1.00[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs10737256	0.84[TSI][hapmap]
rs10911679	0.88[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs12119759	0.87[EUR][1000 genomes]
rs12385701	0.88[EUR][1000 genomes]
rs12566404	0.94[EUR][1000 genomes]
rs1322646	0.84[TSI][hapmap]
rs1407557	0.84[TSI][hapmap]
rs2146329	0.84[TSI][hapmap]
rs2378957	0.83[GIH][hapmap]
rs28609768	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs34463352	0.91[AMR][1000 genomes]
rs34916432	0.88[EUR][1000 genomes]
rs34969721	0.86[EUR][1000 genomes]
rs6674490	0.86[TSI][hapmap]
rs6677056	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs6684586	0.84[TSI][hapmap]
rs6699626	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7523448	0.88[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs950327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7548237	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185127200-185147000	Weak transcription	Spleen	Spleen
2	chr1:185127200-185169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:185127400-185128400	Enhancers	Stomach Mucosa	stomach
4	chr1:185127400-185129200	Weak transcription	HSMM	muscle
5	chr1:185127400-185130400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:185127400-185130400	Weak transcription	Fetal Thymus	thymus
7	chr1:185127400-185133400	Weak transcription	Lung	lung
8	chr1:185127400-185135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:185127400-185135600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:185127400-185136400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:185127400-185144400	Weak transcription	Pancreas	Pancrea
12	chr1:185127400-185152200	Weak transcription	Aorta	Aorta
13	chr1:185127400-185153000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:185127400-185157400	Weak transcription	Small Intestine	intestine
15	chr1:185127400-185163400	Weak transcription	Esophagus	oesophagus
16	chr1:185127400-185192000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:185127600-185128400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:185127600-185128400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:185127600-185128400	Enhancers	Adipose Nuclei	Adipose
20	chr1:185127600-185128400	Enhancers	Brain Anterior Caudate	brain
21	chr1:185127600-185128400	Enhancers	Colon Smooth Muscle	Colon
22	chr1:185127600-185128400	Enhancers	Fetal Lung	lung
23	chr1:185127600-185128400	Enhancers	Rectal Smooth Muscle	rectum
24	chr1:185127600-185128400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:185127600-185128400	Enhancers	Hela-S3	cervix
26	chr1:185127600-185128600	Enhancers	Fetal Heart	heart
27	chr1:185127600-185129200	Enhancers	K562	blood
28	chr1:185127600-185130600	Weak transcription	Primary T cells from cord blood	blood
29	chr1:185127600-185131800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:185127600-185133200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr1:185127600-185133600	Weak transcription	Primary B cells from cord blood	blood
32	chr1:185127600-185134200	Weak transcription	Ovary	ovary
33	chr1:185127600-185135200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:185127600-185135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:185127600-185136400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:185127600-185138400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:185127600-185138800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:185127600-185139200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:185127600-185139400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:185127600-185139400	Weak transcription	Fetal Kidney	kidney
41	chr1:185127600-185144400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:185127600-185144800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:185127600-185145200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:185127600-185145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:185127600-185147400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:185127600-185170000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:185127600-185184600	Weak transcription	Psoas Muscle	Psoas
48	chr1:185127600-185218200	Weak transcription	Right Ventricle	heart
49	chr1:185127800-185128400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:185127800-185128400	Enhancers	Brain Angular Gyrus	brain

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