Variant report

Variant	rs1562217
Chromosome Location	chr1:67073566-67073567
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:67072874..67073739-chr1:67191676..67192371,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1032634	0.91[CEU][hapmap]
rs1032635	0.92[CEU][hapmap]
rs10749763	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10749765	0.96[CEU][hapmap]
rs10789210	0.95[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10789214	0.96[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap]
rs10789215	0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs10889634	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10889635	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]
rs10889641	1.00[CEU][hapmap]
rs10889642	0.96[CEU][hapmap]
rs10889643	0.96[CEU][hapmap]
rs10889644	0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs11208932	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280280	0.92[CEU][hapmap]
rs1280310	0.84[CEU][hapmap]
rs1325261	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1325263	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1329978	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1373911	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1445575	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1536115	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1856318	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2025595	0.96[CEU][hapmap]
rs2031478	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2044400	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2146904	0.92[CEU][hapmap]
rs2147777	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2483704	0.92[CEU][hapmap]
rs2483705	0.92[CEU][hapmap]
rs2872078	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2916	0.84[CEU][hapmap]
rs4488004	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs4655506	0.96[CEU][hapmap];0.84[TSI][hapmap]
rs4655628	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4655631	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4655633	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4655635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655636	0.96[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4655640	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4655646	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4655647	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4655648	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4655650	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap]
rs485521	0.92[CEU][hapmap]
rs499263	0.88[CEU][hapmap]
rs502690	0.87[CEU][hapmap]
rs523132	0.92[CEU][hapmap]
rs523188	0.91[CEU][hapmap]
rs523956	0.92[CEU][hapmap]
rs524114	0.92[CEU][hapmap]
rs536410	0.96[CEU][hapmap]
rs536527	0.92[CEU][hapmap]
rs539014	0.84[CEU][hapmap]
rs602513	0.92[CEU][hapmap]
rs603750	0.92[CEU][hapmap]
rs618093	0.92[CEU][hapmap]
rs628655	0.84[CEU][hapmap]
rs6588207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6588215	0.96[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs659291	0.92[CEU][hapmap]
rs665319	0.92[CEU][hapmap]
rs6656550	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6656912	0.96[CEU][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6659968	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6670378	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6680876	1.00[CEU][hapmap]
rs6680944	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6681460	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6689864	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696927	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6697088	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519747	0.96[CEU][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap]
rs7521111	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7521123	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7524818	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7524851	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528182	0.85[AFR][1000 genomes]
rs7532173	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7542924	0.96[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs7554101	0.92[CEU][hapmap]
rs964574	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9659879	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9662943	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9662962	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs996123	0.83[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
rs1562217	TCTEX1D1	cis	cerebellum	SCAN
rs1562217	ANGPTL3	cis	cerebellum	SCAN
rs1562217	TCTEX1D1	cis	parietal	SCAN
rs1562217	SGIP1	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	chr1:67059200-67074400	Weak transcription	Fetal Lung	lung
3	chr1:67064400-67074600	Weak transcription	Right Ventricle	heart
4	chr1:67065600-67077000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:67065800-67078800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:67065800-67082800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:67066200-67083800	Weak transcription	NHLF	lung
8	chr1:67066400-67089600	Weak transcription	Brain Angular Gyrus	brain
9	chr1:67066600-67073600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:67066600-67077800	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:67068000-67082600	Weak transcription	NHDF-Ad	bronchial
12	chr1:67071200-67075400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:67071400-67073600	Weak transcription	Fetal Heart	heart
14	chr1:67071600-67094800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:67072000-67075200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:67073200-67074400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:67073200-67079000	Weak transcription	Aorta	Aorta
18	chr1:67073400-67073600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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