Variant report

Variant	rs16951398
Chromosome Location	chr17:15245407-15245408
allele	C/T
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	MAX	chr17:15244207-15245443	A549	lung:	n/a	n/a
2	SIN3A	chr17:15244325-15245455	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr17:15244287-15245455	A549	lung:	n/a	chr17:15244855-15244867 chr17:15244935-15244945

Variant related genes	Relation type
TEKT3	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12449596	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12452365	0.92[AMR][1000 genomes]
rs12452683	0.92[AMR][1000 genomes]
rs16951345	0.86[MEX][hapmap]
rs16951377	0.80[ASW][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap]
rs16951380	0.92[AMR][1000 genomes]
rs16951399	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16951402	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16951416	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16951426	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs58893387	0.92[AMR][1000 genomes]
rs73978002	0.92[AMR][1000 genomes]
rs8069939	0.92[AMR][1000 genomes]
rs8077862	1.00[GIH][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv907703	chr17:15199907-15370701	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949172	chr17:15206970-15416808	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15244200-15245600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr17:15244200-15245600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:15244600-15245600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr17:15244600-15245600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr17:15244600-15245800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr17:15244800-15245600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
7	chr17:15245200-15245600	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr17:15245200-15245600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
9	chr17:15245200-15247600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:15245400-15245600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
11	chr17:15245400-15245600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr17:15245400-15245600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr17:15245400-15245600	Active TSS	Adipose Nuclei	Adipose
14	chr17:15245400-15245600	Bivalent Enhancer	Liver	Liver
15	chr17:15245400-15245600	Enhancers	Brain Cingulate Gyrus	brain
16	chr17:15245400-15245600	Enhancers	Brain Substantia Nigra	brain
17	chr17:15245400-15245600	Bivalent Enhancer	Fetal Heart	heart
18	chr17:15245400-15245600	Enhancers	Rectal Smooth Muscle	rectum
19	chr17:15245400-15245600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr17:15245400-15245600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
21	chr17:15245400-15245600	Bivalent Enhancer	A549	lung
22	chr17:15245400-15245600	Bivalent Enhancer	Osteobl	bone
23	chr17:15245400-15245800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr17:15245400-15246000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:15245400-15246400	Enhancers	Placenta	Placenta
26	chr17:15245400-15246400	Enhancers	NHEK	skin
27	chr17:15245400-15246600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr17:15245400-15246800	Weak transcription	HSMM	muscle
29	chr17:15245400-15247200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:15245400-15248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:15245400-15249000	Weak transcription	Fetal Intestine Large	intestine
32	chr17:15245400-15249600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr17:15245400-15251000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links