Variant report

Variant	rs17260781
Chromosome Location	chr1:210943930-210943931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10494929	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1112600	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[MEX][hapmap]
rs1123489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12404442	0.84[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12406602	0.82[AMR][1000 genomes]
rs1418972	0.80[AMR][1000 genomes]
rs1539532	0.80[AMR][1000 genomes]
rs17188548	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17188562	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17188576	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17188617	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17188623	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17260718	0.86[GIH][hapmap]
rs17260795	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17260816	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17260830	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs17260837	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs1934611	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1934619	1.00[GIH][hapmap]
rs3905343	1.00[ASW][hapmap]
rs56102016	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61827576	0.82[AMR][1000 genomes]
rs61827577	0.82[AMR][1000 genomes]
rs61827580	0.82[AMR][1000 genomes]
rs61827581	0.82[AMR][1000 genomes]
rs61829485	0.83[AMR][1000 genomes]
rs61829488	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61829491	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61829494	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6691880	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7523746	0.80[AMR][1000 genomes]
rs7532804	0.82[EUR][1000 genomes]
rs7535110	1.00[ASW][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs7552646	1.00[ASW][hapmap]

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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873153	chr1:210900481-210994339	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv999018	chr1:210907239-210999306	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17260781	KCNH1	cis	parietal	SCAN
rs17260781	DTL	cis	cerebellum	SCAN
rs17260781	ASB9	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210941800-210978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:210943000-210945400	Enhancers	HSMMtube	muscle
3	chr1:210943000-210952800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:210943200-210944200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:210943200-210944400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:210943800-210944400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr1:210943800-210944800	Enhancers	HSMM	muscle

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