Variant report

Variant	rs10889635
Chromosome Location	chr1:67075575-67075576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1032634	0.87[CEU][hapmap]
rs1032635	0.87[CEU][hapmap]
rs10749763	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10749765	0.91[CEU][hapmap]
rs10789210	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10789214	0.92[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap]
rs10789215	0.92[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs10889634	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10889641	0.95[CEU][hapmap]
rs10889642	0.92[CEU][hapmap]
rs10889643	0.92[CEU][hapmap]
rs10889644	0.92[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap]
rs11208932	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280280	0.88[CEU][hapmap]
rs1280310	0.80[CEU][hapmap]
rs1325261	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1325263	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs1329978	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1373911	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1445575	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1536115	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1562217	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1856318	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2025595	0.92[CEU][hapmap]
rs2031478	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2044400	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2146904	0.88[CEU][hapmap]
rs2147777	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2483704	0.88[CEU][hapmap]
rs2483705	0.88[CEU][hapmap]
rs2872078	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2916	0.80[CEU][hapmap]
rs4655506	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs4655628	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655631	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4655633	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4655635	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655636	0.92[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4655646	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4655647	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4655648	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4655650	0.92[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs485521	0.88[CEU][hapmap]
rs499263	0.84[CEU][hapmap]
rs502690	0.83[CEU][hapmap]
rs523132	0.88[CEU][hapmap]
rs523188	0.91[CEU][hapmap]
rs523956	0.88[CEU][hapmap]
rs524114	0.88[CEU][hapmap]
rs536410	0.92[CEU][hapmap]
rs536527	0.88[CEU][hapmap]
rs602513	0.88[CEU][hapmap]
rs603750	0.92[CEU][hapmap]
rs618093	0.87[CEU][hapmap]
rs6588207	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6588215	0.92[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap]
rs659291	0.88[CEU][hapmap]
rs665319	0.88[CEU][hapmap]
rs6656550	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6656912	0.92[CEU][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659968	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6670378	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6680006	0.83[LWK][hapmap];0.82[YRI][hapmap]
rs6680876	0.96[CEU][hapmap]
rs6680944	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6681460	0.96[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6687663	0.80[YRI][hapmap]
rs6689864	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696927	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6697088	0.96[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519747	0.92[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs7521111	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7521123	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7524818	0.96[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524851	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7532173	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7542924	0.92[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs7554101	0.88[CEU][hapmap]
rs964574	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9659879	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9662943	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9662962	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs996123	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10889635	SGIP1	cis	cerebellum	SCAN
rs10889635	TCTEX1D1	cis	parietal	SCAN
rs10889635	ANGPTL3	cis	cerebellum	SCAN
rs10889635	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67058000-67092200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:67065600-67077000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:67065800-67078800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:67065800-67082800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:67066200-67083800	Weak transcription	NHLF	lung
6	chr1:67066400-67089600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:67066600-67077800	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:67068000-67082600	Weak transcription	NHDF-Ad	bronchial
9	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:67073200-67079000	Weak transcription	Aorta	Aorta
11	chr1:67073600-67075800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:67074000-67081200	Weak transcription	Brain Anterior Caudate	brain
13	chr1:67074600-67078000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:67075200-67077400	Weak transcription	Fetal Lung	lung
15	chr1:67075400-67077000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:67075400-67077000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:67075400-67077600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:67075400-67079400	Weak transcription	Fetal Heart	heart

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