Variant report

Variant	rs12633518
Chromosome Location	chr3:48324000-48324001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48236614..48239290-chr3:48321590..48324141,2	K562	blood:
2	chr3:48319259..48321840-chr3:48323712..48326598,2	K562	blood:
3	chr3:48321410..48325314-chr3:48327705..48332086,4	K562	blood:
4	chr3:48322073..48324985-chr3:48594255..48595778,2	MCF-7	breast:
5	chr3:48318319..48320980-chr3:48323069..48325420,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114268	Chromatin interaction
ENSG00000265483	Chromatin interaction
ENSG00000199476	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11130161	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1380053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs1459247	0.82[JPT][hapmap]
rs34136919	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34146962	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34373799	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3731532	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs57994790	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58582477	0.95[EUR][1000 genomes]
rs60305502	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442108	0.83[YRI][hapmap]
rs6442109	0.82[YRI][hapmap]
rs6442122	1.00[YRI][hapmap]
rs6771889	0.82[YRI][hapmap]
rs71323398	0.82[AMR][1000 genomes]
rs73831561	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73831563	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73831566	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[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	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12633518	ZNF589	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48310800-48330200	Weak transcription	Fetal Lung	lung
2	chr3:48311000-48333800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:48311200-48330800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:48311200-48334400	Weak transcription	Aorta	Aorta
5	chr3:48311400-48333400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:48311400-48334200	Weak transcription	Thymus	Thymus
7	chr3:48311600-48330800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:48311600-48334200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:48311600-48334200	Weak transcription	Liver	Liver
10	chr3:48311800-48329800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:48312000-48334400	Weak transcription	Brain Substantia Nigra	brain
12	chr3:48312200-48331000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:48312400-48330200	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:48312400-48334400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:48312600-48333800	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:48312800-48328000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:48312800-48330200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:48312800-48334400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:48313000-48330200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:48313000-48335400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:48313400-48330000	Weak transcription	Fetal Brain Female	brain
22	chr3:48313800-48330200	Weak transcription	Brain Germinal Matrix	brain
23	chr3:48313800-48330800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:48314000-48330200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:48314000-48334200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:48314600-48335800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:48315600-48330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:48318000-48326200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:48318800-48330800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:48320800-48330200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:48321200-48327800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:48321200-48327800	Weak transcription	Primary T cells from cord blood	blood
33	chr3:48321200-48334400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr3:48321400-48327800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:48321400-48327800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:48321400-48334400	Weak transcription	Placenta	Placenta
37	chr3:48321400-48334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:48321600-48334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:48321600-48334400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr3:48321800-48324200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:48322600-48325600	Weak transcription	Osteobl	bone
42	chr3:48322600-48332200	Weak transcription	Adipose Nuclei	Adipose
43	chr3:48322800-48325800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:48323000-48326400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:48323200-48332400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:48323600-48324000	Enhancers	Gastric	stomach
47	chr3:48323600-48324000	Active TSS	Spleen	Spleen
48	chr3:48323600-48324400	Enhancers	Pancreas	Pancrea
49	chr3:48323800-48324000	Enhancers	Esophagus	oesophagus
50	chr3:48323800-48334400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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