Variant report

Variant	rs7547420
Chromosome Location	chr1:185073723-185073724
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:185068561..185071467-chr1:185072156..185075364,3	K562	blood:
2	chr1:185073065..185075023-chr1:185121004..185123409,2	MCF-7	breast:
3	chr1:185063165..185065327-chr1:185071778..185074754,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1046592	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10489580	0.86[JPT][hapmap]
rs1053166	0.80[TSI][hapmap]
rs10737256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10752945	0.87[ASN][1000 genomes]
rs10797998	0.91[CHB][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];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798000	0.81[JPT][hapmap]
rs10911678	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10911679	0.80[TSI][hapmap]
rs10911680	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11588646	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12025737	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12030554	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12081098	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12086086	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs12404187	0.81[JPT][hapmap]
rs12404644	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12566975	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1322646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1407555	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1407556	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1407557	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1544052	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs1884447	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057222	0.90[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[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];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2146329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28609768	0.82[TSI][hapmap]
rs3753569	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4549995	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6424971	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6674490	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6684586	1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap]
rs6700484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7512290	0.81[JPT][hapmap]
rs7519019	1.00[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7523448	0.82[TSI][hapmap]
rs7533198	0.81[JPT][hapmap]
rs7548237	0.82[TSI][hapmap]
rs950327	0.82[TSI][hapmap]

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
rs7547420	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:185016400-185073800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:185018400-185101800	Weak transcription	Fetal Brain Male	brain
3	chr1:185030200-185076600	Weak transcription	Gastric	stomach
4	chr1:185034800-185077000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:185052000-185076200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:185052400-185074800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:185052800-185076600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:185054200-185073800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:185054400-185101800	Weak transcription	A549	lung
10	chr1:185055200-185076600	Weak transcription	Lung	lung
11	chr1:185055400-185096200	Weak transcription	Hela-S3	cervix
12	chr1:185056000-185076800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:185056200-185074200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:185056200-185124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:185056400-185073800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:185056400-185074000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr1:185056600-185074000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:185056600-185077000	Weak transcription	Thymus	Thymus
19	chr1:185057200-185074000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:185057600-185094600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:185058200-185074800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:185058600-185089000	Weak transcription	Ovary	ovary
23	chr1:185058800-185075800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:185058800-185075800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:185058800-185093600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:185059000-185076200	Weak transcription	Brain Germinal Matrix	brain
27	chr1:185059000-185124800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr1:185060800-185074000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:185063000-185076600	Weak transcription	Fetal Brain Female	brain
30	chr1:185064600-185075200	Weak transcription	Psoas Muscle	Psoas
31	chr1:185065800-185088600	Weak transcription	NHDF-Ad	bronchial
32	chr1:185066000-185074200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:185067200-185074400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:185067200-185075200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:185067600-185078400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:185067800-185073800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr1:185067800-185074200	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:185067800-185075800	Weak transcription	Fetal Thymus	thymus
39	chr1:185067800-185076600	Weak transcription	Aorta	Aorta
40	chr1:185067800-185076600	Weak transcription	Spleen	Spleen
41	chr1:185067800-185076800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:185067800-185095400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:185068000-185076600	Weak transcription	GM12878-XiMat	blood
44	chr1:185068400-185110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:185068600-185077000	Weak transcription	HUVEC	blood vessel
46	chr1:185068600-185078200	Weak transcription	K562	blood
47	chr1:185069200-185076000	Weak transcription	Fetal Stomach	stomach
48	chr1:185069400-185076400	Weak transcription	Primary T cells from cord blood	blood
49	chr1:185069400-185076600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:185069400-185079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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