Variant report

Variant	rs4759275
Chromosome Location	chr12:57525756-57525757
allele	A/G
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	MAZ	chr12:57525540-57528414	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:57525756-57526108	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:57520108..57523293-chr12:57525745..57528597,4	MCF-7	breast:
2	chr12:57520290..57524994-chr12:57525334..57528665,7	K562	blood:

Variant related genes	Relation type
STAT6	TF binding region
ENSG00000123384	Chromatin interaction
ENSG00000166888	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10467124	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876963	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172106	0.85[CEU][hapmap];0.80[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172110	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172111	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172113	0.81[TSI][hapmap];0.82[YRI][hapmap]
rs12298170	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12309413	1.00[CEU][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12312693	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12322902	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12368672	0.81[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap]
rs324011	0.80[GIH][hapmap]
rs324013	0.91[GIH][hapmap];0.92[MEX][hapmap]
rs324014	0.85[AMR][1000 genomes]
rs4759276	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv428590	chr12:57329214-57527358	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv832428	chr12:57340609-57535694	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4759275	KIF5A	cis	cerebellum	SCAN
rs4759275	STAT6	cis	lymphoblastoid	seeQTL
rs4759275	ATP5B	cis	cerebellum	SCAN
rs4759275	SMARCC2	cis	cerebellum	SCAN
rs4759275	KRT82	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57522800-57525800	Weak transcription	K562	blood
2	chr12:57523000-57530400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:57523400-57525800	Bivalent Enhancer	Fetal Thymus	thymus
4	chr12:57523400-57526600	Flanking Active TSS	Liver	Liver
5	chr12:57523400-57557200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:57523600-57528200	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr12:57523600-57529600	Enhancers	A549	lung
8	chr12:57523600-57532400	Weak transcription	Pancreas	Pancrea
9	chr12:57523800-57525800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr12:57523800-57525800	Flanking Active TSS	HepG2	liver
11	chr12:57523800-57527000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr12:57523800-57527200	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr12:57523800-57527400	Flanking Active TSS	NH-A	brain
14	chr12:57523800-57529600	Enhancers	Stomach Mucosa	stomach
15	chr12:57523800-57530000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:57523800-57530600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:57523800-57532600	Weak transcription	Gastric	stomach
18	chr12:57523800-57537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:57524000-57526000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:57524000-57526000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:57524000-57526200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:57524000-57526600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:57524000-57527400	Enhancers	Aorta	Aorta
24	chr12:57524000-57528200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr12:57524000-57530400	Enhancers	H9 Cell Line	embryonic stem cell
26	chr12:57524000-57530400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:57524000-57542200	Weak transcription	HMEC	breast
28	chr12:57524000-57543000	Weak transcription	NHEK	skin
29	chr12:57524200-57525800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:57524200-57526600	Weak transcription	Hela-S3	cervix
31	chr12:57524200-57526800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:57524400-57526000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
33	chr12:57524400-57526400	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr12:57524400-57526400	Transcr. at gene 5' and 3'	NHLF	lung
35	chr12:57524400-57527200	Flanking Active TSS	NHDF-Ad	bronchial
36	chr12:57524400-57529200	Genic enhancers	Fetal Stomach	stomach
37	chr12:57524400-57530000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr12:57524600-57526000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:57524600-57526200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:57524600-57526200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:57524600-57526600	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr12:57524600-57529400	Enhancers	Placenta	Placenta
43	chr12:57524600-57530400	Enhancers	Left Ventricle	heart
44	chr12:57524800-57525800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr12:57524800-57525800	Enhancers	Small Intestine	intestine
46	chr12:57524800-57526200	Enhancers	Right Ventricle	heart
47	chr12:57524800-57526200	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr12:57524800-57526200	Transcr. at gene 5' and 3'	Osteobl	bone
49	chr12:57524800-57526400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:57524800-57526400	Enhancers	Lung	lung

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