Variant report

Variant	rs17235791
Chromosome Location	chr15:33447684-33447685
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	PBX3	chr15:33446503-33447720	SK-N-SH	brain:	n/a	n/a
2	EP300	chr15:33446597-33447692	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr15:33446555-33447839	SK-N-SH	brain:	n/a	chr15:33447599-33447606 chr15:33447596-33447606
4	TCF12	chr15:33446652-33447720	SK-N-SH	brain:	n/a	n/a
5	EP300	chr15:33446705-33447772	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr15:33446663-33447708	SK-N-SH	brain:	n/a	n/a
7	RXRA	chr15:33446889-33447687	SK-N-SH	brain:	n/a	n/a
8	JUND	chr15:33446753-33447704	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr15:33446400-33447781	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr15:33446672-33447758	SK-N-SH	brain:	n/a	chr15:33447599-33447606 chr15:33447596-33447606

Variant related genes	Relation type
FMN1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1399077	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1399078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17235784	1.00[ASW][hapmap];0.95[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]
rs713277	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7162655	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7165262	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026162	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027575	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17235791	KLF13	cis	parietal	SCAN
rs17235791	TRPM1	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr15:33442600-33448000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr15:33443800-33450200	Weak transcription	Fetal Intestine Large	intestine
5	chr15:33444600-33447800	Enhancers	HMEC	breast
6	chr15:33445600-33453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:33446000-33449600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:33446200-33448200	Enhancers	Brain Hippocampus Middle	brain
9	chr15:33446400-33448800	Enhancers	Placenta	Placenta
10	chr15:33446600-33447800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:33446600-33447800	Enhancers	NHDF-Ad	bronchial
12	chr15:33446800-33449800	Weak transcription	Lung	lung
13	chr15:33446800-33450200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr15:33447000-33448200	Enhancers	HSMMtube	muscle
15	chr15:33447000-33454600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:33447200-33447800	Enhancers	Rectal Smooth Muscle	rectum
17	chr15:33447200-33449800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:33447400-33447800	Enhancers	Brain Angular Gyrus	brain
19	chr15:33447400-33447800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr15:33447400-33447800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:33447400-33448400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:33447400-33449600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:33447600-33447800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:33447600-33447800	Enhancers	Osteobl	bone
25	chr15:33447600-33448000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr15:33447600-33448200	Enhancers	HSMM	muscle
27	chr15:33447600-33448600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:33447600-33449800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:33447600-33449800	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links