Variant report

Variant	rs1466275
Chromosome Location	chr3:46933266-46933267
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:46933095-46933297	GM19239	blood:	n/a	n/a
2	MAFK	chr3:46933020-46933292	HepG2	liver:	n/a	chr3:46933152-46933167
3	MYC	chr3:46933141-46933298	MCF-7	breast:	n/a	n/a
4	POLR2A	chr3:46931669-46936032	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46923987..46927246-chr3:46931255..46933897,4	K562	blood:
2	chr3:46927679..46930570-chr3:46933189..46935656,3	MCF-7	breast:
3	chr3:46923291..46931131-chr3:46931662..46935716,9	K562	blood:
4	chr3:46929163..46931629-chr3:46932279..46935009,2	K562	blood:
5	chr3:46733775..46736386-chr3:46933231..46935509,2	MCF-7	breast:

Variant related genes	Relation type
PTH1R	TF binding region
ENSG00000268537	TF binding region
ENSG00000160808	Chromatin interaction
ENSG00000178038	Chromatin interaction
ENSG00000268537	Chromatin interaction
ENSG00000160801	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1001284	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865943	0.92[ASN][1000 genomes]
rs1138518	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11705936	0.91[ASN][1000 genomes]
rs11719795	0.94[ASN][1000 genomes]
rs2242116	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290545	0.82[ASN][1000 genomes]
rs2290546	0.91[ASN][1000 genomes]
rs4539969	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4587	0.91[ASN][1000 genomes]
rs4682845	0.92[ASN][1000 genomes]
rs4683296	0.90[ASN][1000 genomes]
rs4683297	0.90[ASN][1000 genomes]
rs4683298	0.92[ASN][1000 genomes]
rs4683299	0.90[ASN][1000 genomes]
rs4683300	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683301	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442038	0.83[ASN][1000 genomes]
rs6442039	0.82[ASN][1000 genomes]
rs6442040	0.90[ASN][1000 genomes]
rs6780601	0.91[ASN][1000 genomes]
rs724448	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724449	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724450	0.95[ASN][1000 genomes]
rs7623898	0.90[ASN][1000 genomes]
rs7635480	0.84[ASN][1000 genomes]
rs7645278	0.90[ASN][1000 genomes]
rs7646906	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9852082	0.90[ASN][1000 genomes]
rs9855938	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1003979	chr3:46853374-46943854	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv590206	chr3:46873957-46935527	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv876753	chr3:46884552-46957298	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1466275	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46926000-46933400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:46926600-46933400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:46930400-46933600	Enhancers	Ovary	ovary
4	chr3:46930400-46933800	Enhancers	Spleen	Spleen
5	chr3:46930600-46933800	Bivalent Enhancer	Placenta	Placenta
6	chr3:46931200-46933400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:46931800-46933400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:46932000-46933400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:46932000-46933400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:46932000-46933600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:46932200-46933600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr3:46932400-46933600	Enhancers	Liver	Liver
13	chr3:46932400-46933800	Enhancers	Gastric	stomach
14	chr3:46932600-46933600	Enhancers	Right Ventricle	heart
15	chr3:46932600-46933800	Enhancers	Right Atrium	heart
16	chr3:46932800-46933400	Enhancers	Fetal Heart	heart
17	chr3:46932800-46933400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr3:46932800-46933600	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr3:46932800-46933800	Enhancers	Esophagus	oesophagus
20	chr3:46932800-46933800	Bivalent Enhancer	Fetal Stomach	stomach
21	chr3:46933000-46933400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
22	chr3:46933000-46933400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr3:46933000-46933600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
24	chr3:46933000-46933600	Enhancers	Left Ventricle	heart
25	chr3:46933000-46933600	Enhancers	Pancreas	Pancrea
26	chr3:46933000-46933800	Enhancers	Lung	lung
27	chr3:46933000-46934800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:46933200-46933400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:46933200-46933400	Enhancers	Adipose Nuclei	Adipose
30	chr3:46933200-46933400	Enhancers	Brain Anterior Caudate	brain
31	chr3:46933200-46933400	Bivalent/Poised TSS	Fetal Brain Male	brain
32	chr3:46933200-46933400	Flanking Active TSS	Fetal Kidney	kidney
33	chr3:46933200-46933400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
34	chr3:46933200-46933400	Bivalent Enhancer	NHDF-Ad	bronchial
35	chr3:46933200-46933600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:46933200-46933600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:46933200-46933600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
38	chr3:46933200-46933600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:46933200-46933600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:46933200-46933600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:46933200-46933600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr3:46933200-46933600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:46933200-46933600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:46933200-46933600	Enhancers	Colon Smooth Muscle	Colon
45	chr3:46933200-46933800	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr3:46933200-46933800	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr3:46933200-46933800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr3:46933200-46934000	Bivalent Enhancer	Stomach Mucosa	stomach
49	chr3:46933200-46934200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:46933200-46934400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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