Variant report

Variant	rs318890
Chromosome Location	chr8:50869707-50869708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11773979	0.81[EUR][1000 genomes]
rs13267366	0.81[CEU][hapmap]
rs1352117	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs1385311	0.89[CEU][hapmap]
rs1484807	1.00[MEX][hapmap]
rs1486258	0.82[TSI][hapmap]
rs167629	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs167630	0.89[CEU][hapmap]
rs172758	0.86[EUR][1000 genomes]
rs17674389	0.90[CEU][hapmap]
rs178543	0.85[EUR][1000 genomes]
rs182646	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2170953	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2200494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs223081	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs2385554	0.85[TSI][hapmap]
rs2385697	0.81[EUR][1000 genomes]
rs2449957	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs2449958	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2450285	0.88[EUR][1000 genomes]
rs2450288	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2450291	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2628417	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2630550	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs318860	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs318862	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs318864	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs318870	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs318871	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs318872	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs318873	0.90[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs318875	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs318877	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs318884	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs318885	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs318888	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs318893	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs318894	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs318902	0.89[CEU][hapmap];0.84[GIH][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs318903	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs318905	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs318906	0.89[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs318908	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs318910	1.00[ASW][hapmap];0.89[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs318911	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs318912	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs365318	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs366526	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs380279	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs384406	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs391798	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs402156	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs406337	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs415276	0.90[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs417918	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs436688	0.89[EUR][1000 genomes]
rs6472722	1.00[CEU][hapmap]
rs967109	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs967110	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs967116	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs993552	0.89[CEU][hapmap];0.87[EUR][1000 genomes]

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	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1022115	chr8:50864995-50981944	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv611311	chr8:50865230-50980320	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs318890	SNTG1	cis	parietal	SCAN
rs318890	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50855200-50875200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr8:50858400-50870200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:50858400-50871600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:50860400-50875400	Weak transcription	Fetal Intestine Small	intestine
5	chr8:50868400-50873200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr8:50868600-50872600	Weak transcription	Brain Germinal Matrix	brain
7	chr8:50869400-50869800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:50869400-50870400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr8:50869400-50870400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:50869600-50870000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr8:50869600-50870200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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