Variant report

Variant	rs12039282
Chromosome Location	chr1:67058323-67058324
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10493411	0.86[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789211	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10889629	0.89[ASN][1000 genomes]
rs10889638	0.87[EUR][1000 genomes]
rs11208907	0.82[ASN][1000 genomes]
rs11208908	0.90[ASN][1000 genomes]
rs11208910	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11208924	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11208929	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208930	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11208937	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs1156618	0.89[ASN][1000 genomes]
rs12021913	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12023176	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12034344	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12041930	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046520	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12402181	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12565798	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12567556	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1373909	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1445573	0.85[CHD][hapmap]
rs1445578	0.81[TSI][hapmap]
rs1445579	0.81[TSI][hapmap]
rs17129064	0.81[TSI][hapmap]
rs1867631	0.83[CHD][hapmap]
rs1925342	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs2312153	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795531	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4655498	0.90[ASN][1000 genomes]
rs4655620	0.90[ASN][1000 genomes]
rs4655630	0.83[CHD][hapmap]
rs6588209	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6588214	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs6680968	0.90[ASN][1000 genomes]
rs6686606	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6687137	0.90[ASN][1000 genomes]
rs6701907	1.00[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6701988	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72918447	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7512692	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519639	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7525509	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7526812	1.00[CEU][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs7535076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537440	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7547794	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7547857	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7547866	0.89[ASN][1000 genomes]
rs7551301	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs963140	0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003016	chr1:67043120-67067119	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1013476	chr1:67044630-67065911	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1221	chr1:67047908-67092696	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12039282	SGIP1	cis	cerebellum	SCAN
rs12039282	ITGB3BP	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67041600-67062400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:67043200-67064400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:67043600-67066600	Weak transcription	Fetal Brain Male	brain
4	chr1:67044200-67064000	Weak transcription	NH-A	brain
5	chr1:67044800-67064000	Weak transcription	Osteobl	bone
6	chr1:67046400-67060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:67049600-67062600	Weak transcription	Psoas Muscle	Psoas
8	chr1:67051000-67060400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:67051000-67061600	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:67051000-67064200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:67051000-67064400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:67051000-67065000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:67051200-67059000	Weak transcription	NHLF	lung
14	chr1:67051200-67063200	Weak transcription	NHDF-Ad	bronchial
15	chr1:67051200-67064200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:67051200-67064400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:67051200-67064400	Weak transcription	Brain Substantia Nigra	brain
18	chr1:67051200-67066200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:67052200-67070800	Weak transcription	Fetal Heart	heart
20	chr1:67053800-67062200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:67055400-67064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:67055400-67073000	Weak transcription	Left Ventricle	heart
23	chr1:67055600-67061400	Weak transcription	Fetal Brain Female	brain
24	chr1:67056200-67061000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:67056800-67059200	Enhancers	HepG2	liver
26	chr1:67057000-67058600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:67057200-67064000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:67057400-67060200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:67057800-67073000	Weak transcription	Aorta	Aorta
30	chr1:67058000-67092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:67058200-67060200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:67058200-67064400	Weak transcription	Brain Anterior Caudate	brain

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