Variant report

Variant	rs10911678
Chromosome Location	chr1:185081903-185081904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1046592	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap]
rs10489580	0.86[JPT][hapmap]
rs10737256	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10752945	0.94[ASN][1000 genomes]
rs10797998	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs10797999	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798000	0.81[JPT][hapmap]
rs10911680	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11588646	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12025737	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12030554	0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12081098	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12086086	0.86[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs12404187	0.81[JPT][hapmap]
rs12404644	0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs12566975	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1322646	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1407555	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1407556	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1407557	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1544052	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs1884447	0.90[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[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];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057222	0.90[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2146329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753569	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4549995	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6424971	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6424972	0.83[CHD][hapmap]
rs6674490	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6677056	0.82[TSI][hapmap]
rs6684586	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs6700484	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7512290	0.81[JPT][hapmap]
rs7519019	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7523448	0.80[TSI][hapmap]
rs7533198	0.81[JPT][hapmap]
rs7547420	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7548237	0.80[TSI][hapmap]
rs950327	0.80[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	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
rs10911678	QSOX1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

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	chr1:185065800-185088600	Weak transcription	NHDF-Ad	bronchial
10	chr1:185067800-185095400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:185068400-185110200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:185069400-185091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:185069600-185088200	Weak transcription	Fetal Lung	lung
14	chr1:185070000-185101400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:185070200-185088800	Weak transcription	HSMM	muscle
16	chr1:185070400-185089200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:185073600-185088200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:185073600-185092800	Weak transcription	Fetal Kidney	kidney
19	chr1:185073600-185115000	Weak transcription	NH-A	brain
20	chr1:185073800-185088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:185073800-185088600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:185074000-185088600	Weak transcription	NHLF	lung
23	chr1:185077400-185088200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:185077800-185086400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:185078800-185088800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:185078800-185102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:185079800-185102000	Weak transcription	Small Intestine	intestine
28	chr1:185080000-185101000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr1:185081200-185091400	Weak transcription	GM12878-XiMat	blood
30	chr1:185081600-185091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:185081800-185088600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:185081800-185088800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr1:185081800-185092800	Weak transcription	HUVEC	blood vessel

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