Variant report

Variant	rs12594079
Chromosome Location	chr15:33448065-33448066
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	JUND	chr15:33447893-33448093	HepG2	liver:	n/a	chr15:33447993-33448002

Variant related genes	Relation type
FMN1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11072234	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11636386	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12439207	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12439289	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12439352	0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12592365	0.82[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap]
rs1454986	0.80[ASN][1000 genomes]
rs17235533	1.00[ASW][hapmap]
rs17235638	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17235645	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17235652	0.80[ASN][1000 genomes]
rs17235701	0.88[CEU][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17235708	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs17235722	0.88[CEU][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1902149	0.85[ASN][1000 genomes]
rs1902150	0.85[ASN][1000 genomes]
rs1902151	0.84[AFR][1000 genomes]
rs1988447	0.81[CEU][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs28375098	0.80[ASN][1000 genomes]
rs28420167	0.80[ASN][1000 genomes]
rs28522640	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs28593387	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3850097	0.81[CEU][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs3861196	0.84[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3861200	0.81[CEU][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs4567671	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4780080	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7178163	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv903983	chr15:33388030-33550256	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12594079	KLF13	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33438600-33449800	Weak transcription	NHEK	skin
2	chr15:33441200-33451800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:33443800-33450200	Weak transcription	Fetal Intestine Large	intestine
4	chr15:33445600-33453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:33446000-33449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:33446200-33448200	Enhancers	Brain Hippocampus Middle	brain
7	chr15:33446400-33448800	Enhancers	Placenta	Placenta
8	chr15:33446800-33449800	Weak transcription	Lung	lung
9	chr15:33446800-33450200	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:33447000-33448200	Enhancers	HSMMtube	muscle
11	chr15:33447000-33454600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:33447200-33449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:33447400-33448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:33447400-33449600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:33447600-33448200	Enhancers	HSMM	muscle
16	chr15:33447600-33448600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:33447600-33449800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:33447600-33449800	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr15:33447800-33448400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:33447800-33449800	Weak transcription	HMEC	breast
21	chr15:33447800-33452400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:33447800-33453200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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