Variant report

Variant	rs4130473
Chromosome Location	chr3:51212912-51212913
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10510757	0.83[CHB][hapmap]
rs12485331	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12485754	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487468	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12487496	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488700	0.93[JPT][hapmap]
rs12489219	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12490026	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12491206	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12491836	1.00[EUR][1000 genomes]
rs12492615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493034	0.89[EUR][1000 genomes]
rs12493323	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12493359	0.89[EUR][1000 genomes]
rs12493978	0.89[CHB][hapmap]
rs12495561	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[EUR][1000 genomes]
rs12496621	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12496830	0.89[EUR][1000 genomes]
rs1480366	0.91[YRI][hapmap]
rs17051685	1.00[YRI][hapmap]
rs1809388	0.89[EUR][1000 genomes]
rs1842394	0.95[CHB][hapmap]
rs2086395	0.89[EUR][1000 genomes]
rs2101056	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2127654	1.00[EUR][1000 genomes]
rs2170177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes]
rs2306430	0.90[CHB][hapmap]
rs2306431	0.89[CHB][hapmap]
rs2355946	0.84[EUR][1000 genomes]
rs3762711	1.00[EUR][1000 genomes]
rs4323036	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs4346580	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4468966	0.89[CHB][hapmap]
rs4927961	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4927975	0.84[YRI][hapmap]
rs4974096	0.89[CHB][hapmap]
rs4974100	0.89[EUR][1000 genomes]
rs4974112	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs56052360	0.89[EUR][1000 genomes]
rs57406588	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58720544	0.89[EUR][1000 genomes]
rs58911602	0.89[EUR][1000 genomes]
rs59682667	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59834534	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59957657	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60128296	0.84[EUR][1000 genomes]
rs60461297	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60567238	0.89[EUR][1000 genomes]
rs60740654	0.89[EUR][1000 genomes]
rs60882641	0.89[EUR][1000 genomes]
rs6792254	0.89[EUR][1000 genomes]
rs72936442	0.89[EUR][1000 genomes]
rs72936462	0.84[EUR][1000 genomes]
rs72941919	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72943130	0.89[EUR][1000 genomes]
rs72943137	0.89[EUR][1000 genomes]
rs72943166	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72948197	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72948200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72953143	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72953162	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72953175	1.00[EUR][1000 genomes]
rs7372342	0.89[EUR][1000 genomes]
rs7427615	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap]
rs751076	0.83[CHB][hapmap]
rs880477	1.00[YRI][hapmap]
rs880478	0.90[CHB][hapmap]
rs9817077	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9817872	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs9819195	0.89[CHB][hapmap]
rs9829057	0.89[CHB][hapmap]
rs9856134	0.89[CHB][hapmap]
rs9878592	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][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	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4130473	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51209600-51213200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
2	chr3:51210000-51213000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:51210400-51213600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:51211000-51215200	Weak transcription	Left Ventricle	heart
5	chr3:51211200-51213000	Strong transcription	Brain Hippocampus Middle	brain
6	chr3:51211200-51214000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:51211400-51213800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:51211400-51214000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:51211600-51218600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:51211800-51213000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
11	chr3:51212000-51213000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:51212000-51213000	Strong transcription	Brain Anterior Caudate	brain
13	chr3:51212200-51213000	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr3:51212400-51215000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:51212600-51215000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:51212800-51213800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:51212800-51218200	Weak transcription	Brain Germinal Matrix	brain

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