Variant report

Variant	rs12625736
Chromosome Location	chr20:40752568-40752569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1569552	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17221018	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17221137	0.89[ASW][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17312515	0.89[ASW][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2206167	0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4281967	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs55978324	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6124418	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6130042	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6130043	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6130047	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6130049	0.95[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs73114443	0.92[ASN][1000 genomes]

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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12625736	KCNS1	cis	parietal	SCAN
rs12625736	IFT52	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40715800-40757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40747200-40758400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr20:40747800-40762400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:40752000-40752800	Enhancers	Fetal Brain Female	brain
5	chr20:40752400-40753200	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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