Variant report

Variant	rs1564374
Chromosome Location	chr12:58010163-58010164
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57911754..57916322-chr12:58006406..58010716,5	K562	blood:
2	chr12:58007372..58011848-chr12:58013286..58019253,6	MCF-7	breast:
3	chr12:58009848..58012356-chr12:58118975..58121392,2	MCF-7	breast:
4	chr12:57912181..57914315-chr12:58008996..58011925,2	MCF-7	breast:
5	chr12:53772778..53775585-chr12:58009878..58011429,2	MCF-7	breast:
6	chr12:57913428..57916180-chr12:58009743..58011363,2	MCF-7	breast:
7	chr12:58007718..58010411-chr12:58087376..58090012,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166987	Chromatin interaction
ENSG00000257499	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000185591	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000135502	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000135506	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1027315	0.94[ASN][1000 genomes]
rs1038914	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1050045	0.90[JPT][hapmap]
rs1552842	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1873919	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277324	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2307095	0.96[ASN][1000 genomes]
rs2640610	0.87[ASN][1000 genomes]
rs34271193	0.83[ASN][1000 genomes]
rs6581147	0.81[ASN][1000 genomes]
rs7134861	0.83[ASN][1000 genomes]
rs7295422	0.90[JPT][hapmap]
rs7304145	0.91[ASN][1000 genomes]
rs7311632	0.90[JPT][hapmap]
rs7966795	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs799265	0.90[JPT][hapmap]
rs903067	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs923828	0.89[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1564374	DKFZP586D0919	cis	multi-tissue	Pritchard
rs1564374	FAM119B	cis	cerebellum	SCAN
rs1564374	FAM119B	cis	lymphoblastoid	seeQTL
rs1564374	TSPAN31	cis	brain	seeQTL
rs1564374	XRCC6BP1	cis	multi-tissue	Pritchard
rs1564374	TENC1	cis	cerebellum	SCAN
rs1564374	OR6C4	cis	cerebellum	SCAN
rs1564374	TSPAN31	cis	cerebellum	SCAN
rs1564374	XRCC6BP1	cis	brain	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58005600-58011400	Weak transcription	Lung	lung
2	chr12:58005600-58013200	Weak transcription	Gastric	stomach
3	chr12:58006200-58010200	Weak transcription	NHDF-Ad	bronchial
4	chr12:58006200-58010400	Weak transcription	NH-A	brain
5	chr12:58006200-58014800	Weak transcription	Brain Angular Gyrus	brain
6	chr12:58006400-58011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:58006600-58011000	Strong transcription	Fetal Lung	lung
8	chr12:58006600-58013200	Weak transcription	Pancreas	Pancrea
9	chr12:58006800-58010200	Weak transcription	Fetal Brain Male	brain
10	chr12:58006800-58011400	Strong transcription	Ovary	ovary
11	chr12:58006800-58011600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:58006800-58011600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:58006800-58011600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:58006800-58011800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:58006800-58012000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:58007000-58012000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:58007200-58011200	Strong transcription	Fetal Brain Female	brain
18	chr12:58007400-58010200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:58007600-58010600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:58008000-58010800	Strong transcription	Brain Germinal Matrix	brain
21	chr12:58008000-58011400	Strong transcription	Fetal Stomach	stomach
22	chr12:58008000-58012800	Weak transcription	HepG2	liver
23	chr12:58008200-58010600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:58008400-58010600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:58008400-58012000	Strong transcription	Aorta	Aorta
26	chr12:58008600-58010200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:58008600-58010400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr12:58008600-58010400	Genic enhancers	Stomach Smooth Muscle	stomach
29	chr12:58009000-58010200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:58009000-58010200	Strong transcription	Brain Cingulate Gyrus	brain
31	chr12:58009000-58010800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:58009000-58010800	Strong transcription	Brain Anterior Caudate	brain
33	chr12:58009200-58011200	Strong transcription	Fetal Muscle Trunk	muscle
34	chr12:58009200-58011800	Strong transcription	Colon Smooth Muscle	Colon
35	chr12:58009400-58010400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
36	chr12:58009400-58010400	Genic enhancers	Spleen	Spleen
37	chr12:58009400-58010400	Strong transcription	NHLF	lung
38	chr12:58009400-58010600	Strong transcription	Brain Hippocampus Middle	brain
39	chr12:58009400-58012000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:58009600-58010200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:58009600-58010400	Strong transcription	Rectal Smooth Muscle	rectum
42	chr12:58009600-58010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:58009600-58010600	Strong transcription	Fetal Muscle Leg	muscle
44	chr12:58009800-58010600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:58009800-58010800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr12:58009800-58011800	Active TSS	Left Ventricle	heart
47	chr12:58010000-58010200	Bivalent Enhancer	Placenta	Placenta
48	chr12:58010000-58010200	Strong transcription	Right Ventricle	heart
49	chr12:58010000-58010400	Strong transcription	Brain Substantia Nigra	brain
50	chr12:58010000-58010600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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