Variant report

Variant	rs9516625
Chromosome Location	chr13:96581766-96581767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96575800..96578505-chr13:96580994..96583120,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs3125431	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs475882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs495214	0.89[CEU][hapmap]
rs526702	0.89[CEU][hapmap]
rs534010	0.86[CEU][hapmap]
rs534429	0.89[CEU][hapmap]
rs540213	0.89[CEU][hapmap]
rs565851	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs662884	0.89[CEU][hapmap]
rs674565	0.89[CEU][hapmap]
rs675144	0.89[CEU][hapmap]
rs7332078	0.84[EUR][1000 genomes]
rs7335209	0.84[EUR][1000 genomes]
rs7985727	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816142	0.88[CEU][hapmap]
rs9590318	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs9590331	0.85[CHB][hapmap];0.89[JPT][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	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9516625	DZIP1	cis	parietal	SCAN
rs9516625	UGGT2	cis	cerebellum	SCAN
rs9516625	UGGT2	cis	lymphoblastoid	seeQTL
rs9516625	GPC5	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:96543000-96581800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
6	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
7	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
8	chr13:96559600-96583000	Weak transcription	Pancreas	Pancrea
9	chr13:96559600-96586400	Weak transcription	A549	lung
10	chr13:96559800-96583400	Weak transcription	Esophagus	oesophagus
11	chr13:96559800-96588600	Weak transcription	Gastric	stomach
12	chr13:96566800-96587000	Weak transcription	Colon Smooth Muscle	Colon
13	chr13:96568600-96582000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:96568600-96582800	Weak transcription	Left Ventricle	heart
15	chr13:96568600-96583000	Weak transcription	Ovary	ovary
16	chr13:96571000-96588600	Weak transcription	Psoas Muscle	Psoas
17	chr13:96577000-96581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:96577000-96623200	Weak transcription	NHLF	lung
19	chr13:96577200-96581800	Weak transcription	Fetal Heart	heart
20	chr13:96577200-96582000	Weak transcription	HSMMtube	muscle
21	chr13:96577200-96582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:96577200-96583000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr13:96577200-96585600	Weak transcription	NHDF-Ad	bronchial
24	chr13:96577200-96587600	Weak transcription	HepG2	liver
25	chr13:96577200-96598000	Weak transcription	HMEC	breast
26	chr13:96577600-96582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr13:96577800-96608800	Weak transcription	NHEK	skin
28	chr13:96579000-96581800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr13:96579000-96581800	Weak transcription	Osteobl	bone
30	chr13:96579000-96587200	Weak transcription	NH-A	brain
31	chr13:96579000-96587600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr13:96580600-96582000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:96580600-96582000	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr13:96580600-96585000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
35	chr13:96580600-96585400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
36	chr13:96580800-96582200	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr13:96580800-96583400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:96580800-96583800	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr13:96580800-96585600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr13:96580800-96588600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:96581000-96582400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:96581000-96582400	ZNF genes & repeats	Brain Germinal Matrix	brain
43	chr13:96581000-96583600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
44	chr13:96581400-96582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:96581400-96583600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr13:96581400-96584200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr13:96581600-96581800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr13:96581600-96582000	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr13:96581600-96582000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr13:96581600-96582000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell

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