Variant report

Variant	rs7546472
Chromosome Location	chr1:210996658-210996659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11119614	0.85[JPT][hapmap]
rs12078503	0.86[JPT][hapmap]
rs1343143	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1343150	0.86[JPT][hapmap]
rs17016986	0.86[JPT][hapmap]
rs1770213	0.88[CEU][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes]
rs1770216	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1770219	0.88[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1770221	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs1770222	0.82[EUR][1000 genomes]
rs1777243	0.88[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1777245	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs1777246	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1777258	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1777260	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1777264	0.82[CEU][hapmap];0.86[GIH][hapmap]
rs1890840	0.88[CEU][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1934628	0.81[GIH][hapmap];0.82[MEX][hapmap]
rs1934629	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs1934636	0.86[GIH][hapmap];0.88[MEX][hapmap]
rs2798147	0.88[CEU][hapmap]
rs4951615	0.88[CEU][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4951640	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs6658580	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6666042	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7515909	0.94[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545932	0.86[JPT][hapmap]
rs7553542	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv832503	chr1:210948760-211103163	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7546472	KCNH1	cis	cerebellum	SCAN
rs7546472	LEMD1	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210995400-210996800	Enhancers	Brain Angular Gyrus	brain
2	chr1:210995400-210996800	Enhancers	Brain Cingulate Gyrus	brain
3	chr1:210995400-210997200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:210996000-210996800	Enhancers	Brain Anterior Caudate	brain
5	chr1:210996000-210996800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:210996000-210997000	Enhancers	Liver	Liver
7	chr1:210996000-210997000	Enhancers	Brain Substantia Nigra	brain
8	chr1:210996000-210997200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr1:210996200-210996800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:210996400-210996800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr1:210996400-210996800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:210996600-211015000	Weak transcription	Brain Hippocampus Middle	brain

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