Variant report

Variant	rs10737256
Chromosome Location	chr1:185123630-185123631
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr1:185123416-185123825	HepG2	liver:	n/a	n/a
2	TBP	chr1:185123597-185123690	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:185014501..185017888-chr1:185123055..185126846,5	MCF-7	breast:
2	chr1:185122329..185126145-chr1:185137203..185141899,4	K562	blood:
3	chr1:185012738..185017820-chr1:185123187..185127311,9	K562	blood:
4	chr1:185122925..185124653-chr20:52755101..52757157,2	MCF-7	breast:
5	chr1:185121566..185123829-chr1:185138646..185140537,2	K562	blood:
6	chr1:185112945..185115248-chr1:185120909..185123637,2	MCF-7	breast:
7	chr1:185122996..185124550-chr1:185124586..185126416,2	K562	blood:

No data

Variant related genes	Relation type
SWT1	TF binding region
ENSG00000116668	Chromatin interaction
ENSG00000121481	Chromatin interaction
ENSG00000121486	Chromatin interaction
ENSG00000231084	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1046592	0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs10489580	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs1053166	0.82[TSI][hapmap]
rs10752945	0.90[ASN][1000 genomes]
rs10797998	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs10797999	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798000	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs10911678	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10911679	0.82[TSI][hapmap]
rs10911680	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11588646	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12025737	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12030554	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12081098	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12086086	0.91[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs12404187	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs12404644	0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs12566975	0.98[ASN][1000 genomes]
rs1322646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1407556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1407557	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544052	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs1884447	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2057222	0.90[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2146329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3753569	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4549995	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6424971	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6424972	0.83[CHD][hapmap]
rs6660169	0.81[CHD][hapmap]
rs6673303	0.81[CHD][hapmap]
rs6674490	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6684586	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs6700484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7512290	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7519019	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.90[ASN][1000 genomes]
rs7523448	0.84[TSI][hapmap]
rs7533198	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7547420	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7548237	0.84[TSI][hapmap]
rs950327	0.84[TSI][hapmap]

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	nsv548397	chr1:185104842-185123630	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10737256	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:185082600-185125400	Weak transcription	Spleen	Spleen
4	chr1:185084200-185124400	Weak transcription	Right Ventricle	heart
5	chr1:185085400-185125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:185087000-185125000	Weak transcription	Gastric	stomach
7	chr1:185089400-185124400	Weak transcription	Colonic Mucosa	Colon
8	chr1:185101600-185125200	Weak transcription	Esophagus	oesophagus
9	chr1:185102400-185124400	Weak transcription	Brain Germinal Matrix	brain
10	chr1:185102600-185124400	Weak transcription	Fetal Brain Male	brain
11	chr1:185102600-185124400	Weak transcription	Small Intestine	intestine
12	chr1:185102800-185125000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:185103000-185124400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:185103600-185123800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:185103600-185124400	Weak transcription	Brain Substantia Nigra	brain
16	chr1:185104600-185125000	Weak transcription	Pancreas	Pancrea
17	chr1:185105600-185125200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:185105600-185125200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:185105600-185125200	Weak transcription	Lung	lung
20	chr1:185106000-185124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:185109200-185124400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:185110800-185124400	Weak transcription	Fetal Stomach	stomach
23	chr1:185111400-185123800	Weak transcription	NHLF	lung
24	chr1:185111600-185124400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:185111600-185124400	Weak transcription	Psoas Muscle	Psoas
26	chr1:185112000-185124400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:185115000-185123800	Weak transcription	Fetal Kidney	kidney
28	chr1:185115200-185125000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:185116200-185123800	Weak transcription	A549	lung
30	chr1:185117000-185123800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:185117000-185124200	Weak transcription	Fetal Brain Female	brain
32	chr1:185117400-185123800	Weak transcription	Brain Angular Gyrus	brain
33	chr1:185117600-185125200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:185118400-185124400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:185118600-185124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:185118800-185123800	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:185118800-185125000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:185119600-185124400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:185119800-185124200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:185120000-185123800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:185120000-185124000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:185120000-185124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:185120000-185124800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:185120200-185124000	Weak transcription	Adipose Nuclei	Adipose
45	chr1:185120200-185124400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:185120200-185124400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:185120200-185124400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr1:185120200-185124400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr1:185120200-185124400	Weak transcription	Thymus	Thymus
50	chr1:185120200-185125000	Weak transcription	Ovary	ovary

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