Variant report

Variant	rs4759393
Chromosome Location	chr12:123282532-123282533
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10773627	0.81[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs11059711	0.86[CHB][hapmap]
rs11059724	0.82[ASN][1000 genomes]
rs11059932	0.81[ASN][1000 genomes]
rs11060064	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs11060065	0.86[CHB][hapmap];0.90[CHD][hapmap];0.84[ASN][1000 genomes]
rs12255	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap]
rs12297553	0.89[ASN][1000 genomes]
rs12298293	0.91[ASN][1000 genomes]
rs12305822	0.86[CHB][hapmap]
rs12307038	0.86[CHB][hapmap]
rs12310386	0.86[CHB][hapmap]
rs12312837	0.86[CHB][hapmap]
rs12313006	0.81[CHB][hapmap]
rs12313538	0.90[ASN][1000 genomes]
rs12313600	0.90[ASN][1000 genomes]
rs12314544	0.86[CHB][hapmap]
rs12315520	0.91[ASN][1000 genomes]
rs12318871	0.90[ASN][1000 genomes]
rs12321131	0.84[ASN][1000 genomes]
rs12321556	0.86[CHB][hapmap]
rs1260120	0.82[ASN][1000 genomes]
rs1671688	0.82[ASN][1000 genomes]
rs1696320	0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1696326	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs1799618	0.81[CHB][hapmap];0.87[CHD][hapmap]
rs2135014	0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap]
rs2253504	0.80[ASN][1000 genomes]
rs2271050	0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap]
rs2271051	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs2292134	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs2292136	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2649902	0.82[ASN][1000 genomes]
rs2936730	0.83[ASN][1000 genomes]
rs3817095	0.86[CHB][hapmap]
rs3825143	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs3852537	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs4759355	0.81[ASW][hapmap];0.83[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap]
rs4759382	0.83[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap]
rs4759389	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs4759392	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58182048	0.84[ASN][1000 genomes]
rs6489240	0.84[ASN][1000 genomes]
rs6489245	0.83[CEU][hapmap]
rs6489247	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs652533	0.81[ASN][1000 genomes]
rs7138398	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs7139055	0.83[CEU][hapmap]
rs7294991	0.81[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7309225	0.83[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[ASN][1000 genomes]
rs7311386	0.85[CHB][hapmap]
rs7486414	0.81[CHB][hapmap]
rs7972447	0.83[CEU][hapmap]
rs839360	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs839363	0.84[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs897391	0.81[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs897393	0.81[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs921808	0.81[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs9645762	0.80[ASN][1000 genomes]
rs9788290	0.82[ASN][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	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4759393	HIP1R	cis	parietal	SCAN
rs4759393	CCDC62	cis	cerebellum	SCAN
rs4759393	CCDC62	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123259400-123310600	Weak transcription	HSMMtube	muscle
2	chr12:123259800-123285800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:123259800-123310600	Weak transcription	Brain Substantia Nigra	brain
4	chr12:123260000-123303600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr12:123260200-123284000	Weak transcription	Primary B cells from cord blood	blood
6	chr12:123260200-123284000	Weak transcription	Primary T cells from cord blood	blood
7	chr12:123264200-123290800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:123265600-123303600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:123266000-123303800	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:123274600-123288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:123278600-123283800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:123278600-123284200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:123278600-123305600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:123278800-123283600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:123278800-123283800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:123280800-123284200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr12:123282000-123283800	Weak transcription	Primary monocytes fromperipheralblood	blood

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