Variant report

Variant	rs17234937
Chromosome Location	chr12:48838993-48838994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11168585	0.82[AFR][1000 genomes]
rs11168613	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12306781	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs12578360	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12579547	1.00[CHB][hapmap]
rs12580814	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12580859	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12581223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582586	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582594	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12582811	1.00[CHB][hapmap]
rs2705127	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28889727	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4397895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4426170	1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4547144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55647233	0.90[ASN][1000 genomes]
rs55667337	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55971664	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55983865	0.96[EUR][1000 genomes]
rs56034252	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56191575	0.97[EUR][1000 genomes]
rs59337124	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940763	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940764	0.97[EUR][1000 genomes]
rs61940766	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940767	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940768	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61940776	0.97[EUR][1000 genomes]
rs61940777	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61940779	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61940780	0.97[EUR][1000 genomes]
rs61940822	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61942786	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942812	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942813	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942816	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942817	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61942828	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942830	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942831	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73296804	0.82[AFR][1000 genomes]
rs73296814	0.82[AFR][1000 genomes]
rs73296825	0.86[AFR][1000 genomes]

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	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17234937	KCNH3	cis	cerebellum	SCAN
rs17234937	C12orf62	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48833800-48840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48834200-48840400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48834200-48840400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48836400-48839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:48836600-48839600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48836600-48839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:48836800-48839800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:48837200-48839400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48837800-48839600	Weak transcription	Hela-S3	cervix
10	chr12:48838600-48839400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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