Variant report

Variant	rs12792638
Chromosome Location	chr11:57751354-57751355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1113334	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1113335	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11600060	0.87[CEU][hapmap]
rs11601202	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601223	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601663	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11601841	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs11602442	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11604473	0.87[CEU][hapmap]
rs11604630	0.87[CEU][hapmap]
rs11605988	0.95[ASN][1000 genomes]
rs11606464	0.95[ASN][1000 genomes]
rs11607308	0.87[ASN][1000 genomes]
rs11608016	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12419176	0.91[EUR][1000 genomes]
rs12421773	0.89[EUR][1000 genomes]
rs12788836	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12790525	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12792435	0.95[ASN][1000 genomes]
rs12801976	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12803905	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12804093	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12805812	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs1376489	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs1397273	0.91[EUR][1000 genomes]
rs17152364	0.81[MEX][hapmap]
rs17152376	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs1814059	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs2089747	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2441952	0.81[CEU][hapmap]
rs34015013	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34300518	0.87[ASN][1000 genomes]
rs34563263	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34594669	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35163247	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35713433	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35742790	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36071925	0.95[ASN][1000 genomes]
rs3853676	0.82[MEX][hapmap]
rs4509781	0.91[CEU][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap]
rs56055377	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs609154	0.88[EUR][1000 genomes]
rs61903966	0.95[ASN][1000 genomes]
rs61903967	0.95[ASN][1000 genomes]
rs61904009	0.92[ASN][1000 genomes]
rs61904011	0.87[ASN][1000 genomes]
rs61904024	0.87[ASN][1000 genomes]
rs61905309	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66813766	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7109912	0.91[EUR][1000 genomes]
rs7113760	0.91[CEU][hapmap]
rs7120442	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs7121128	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7123570	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7123727	0.95[ASN][1000 genomes]
rs7126334	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs714942	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7926878	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7927022	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7929515	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7930102	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs7930234	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7934184	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs7935428	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs7936212	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7938062	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs7945154	0.85[CEU][hapmap]
rs7949558	0.87[CEU][hapmap]
rs7950003	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs930703	0.87[CEU][hapmap];0.88[MEX][hapmap]
rs938011	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv328	chr11:57744748-57789940	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12792638	YPEL4	cis	multi-tissue	Pritchard
rs12792638	MS4A10	cis	cerebellum	SCAN
rs12792638	OR5M8	cis	cerebellum	SCAN
rs12792638	DDB1	cis	cerebellum	SCAN
rs12792638	MS4A7	cis	parietal	SCAN
rs12792638	UBE2L6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57749400-57751400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:57749400-57752200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr11:57749800-57758800	Weak transcription	HepG2	liver
4	chr11:57750800-57751400	Enhancers	Fetal Muscle Leg	muscle
5	chr11:57750800-57751600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:57751000-57751400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:57751000-57751400	Enhancers	Adipose Nuclei	Adipose
8	chr11:57751000-57752200	Enhancers	Brain Germinal Matrix	brain
9	chr11:57751200-57751400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:57751200-57751600	Enhancers	Brain Anterior Caudate	brain
11	chr11:57751200-57751600	Enhancers	Left Ventricle	heart

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