Variant report

Variant	rs17748317
Chromosome Location	chr15:42393169-42393170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42384743..42386720-chr15:42391434..42393196,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12148416	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17690109	0.83[CEU][hapmap]
rs17690827	0.92[CEU][hapmap]
rs17690899	0.92[CEU][hapmap]
rs17691880	0.96[EUR][1000 genomes]
rs17747505	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs17748059	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17748132	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2412656	0.92[CEU][hapmap]
rs35200589	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4923926	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923927	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4923928	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924609	0.91[GIH][hapmap]
rs4924611	0.85[CEU][hapmap]
rs4924614	0.90[CEU][hapmap]
rs4924617	0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs4924619	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924620	0.92[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7162019	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7165458	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7165460	0.92[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7166093	0.83[EUR][1000 genomes]
rs7166789	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7168863	0.91[CEU][hapmap]
rs7176443	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176459	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7177034	0.82[CEU][hapmap]
rs750051	0.92[CEU][hapmap]
rs750052	0.92[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs755599	0.92[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap]
rs8029713	0.90[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8042953	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
3	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats 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	73 gene(s)	inside rSNPs	diseases
6	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv904132	chr15:42343794-42398046	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17748317	IVD	cis	parietal	SCAN
rs17748317	GPR176	cis	cerebellum	SCAN
rs17748317	RTF1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42386000-42397600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:42389600-42396400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:42391600-42393600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr15:42392000-42393200	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:42392000-42393200	Enhancers	HUVEC	blood vessel
6	chr15:42392000-42393200	Enhancers	NHEK	skin
7	chr15:42392000-42393400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr15:42392200-42393200	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr15:42392200-42393200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:42392200-42393200	Enhancers	Placenta	Placenta
11	chr15:42392200-42393200	Enhancers	Gastric	stomach
12	chr15:42392200-42393200	Enhancers	Lung	lung
13	chr15:42392200-42393200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr15:42392200-42393200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr15:42392200-42393800	Enhancers	Stomach Mucosa	stomach
16	chr15:42392400-42393200	Enhancers	Primary B cells from cord blood	blood
17	chr15:42392400-42393200	Enhancers	Adipose Nuclei	Adipose
18	chr15:42392400-42393200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr15:42392400-42393200	Enhancers	Spleen	Spleen
20	chr15:42392400-42393400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr15:42392400-42395000	Enhancers	NH-A	brain
22	chr15:42392400-42395200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:42392600-42393200	Enhancers	Colonic Mucosa	Colon
24	chr15:42392600-42393200	Enhancers	Esophagus	oesophagus
25	chr15:42392600-42393200	Enhancers	Left Ventricle	heart
26	chr15:42392600-42393600	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:42392800-42393200	Enhancers	Fetal Muscle Leg	muscle
28	chr15:42392800-42393400	Enhancers	HepG2	liver
29	chr15:42392800-42394200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:42392800-42394600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:42393000-42393600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr15:42393000-42394400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:42393000-42394600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:42393000-42394600	Weak transcription	Hela-S3	cervix
35	chr15:42393000-42394600	Weak transcription	HMEC	breast
36	chr15:42393000-42396800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:42393000-42399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:42393000-42399600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:42393000-42399800	Weak transcription	Right Atrium	heart

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