Variant report

Variant	rs13300981
Chromosome Location	chr9:15294073-15294074
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15293831..15297894-chr9:15305171..15308300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13286025	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13292233	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13293198	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16932961	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16932962	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16932963	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16932968	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16932971	0.93[EUR][1000 genomes]
rs16932980	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16932982	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2199599	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34905481	0.84[AMR][1000 genomes]
rs36086967	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3866794	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3866795	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3905248	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4259499	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs562177	1.00[CHB][hapmap]
rs575442	0.85[CHB][hapmap]
rs585002	0.85[CHB][hapmap]
rs59781734	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62570841	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62570851	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62570852	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs638491	0.85[CHB][hapmap]
rs641579	0.85[CHB][hapmap]
rs693223	0.82[CHB][hapmap]
rs7021480	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7022005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7022190	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7035671	0.85[CHB][hapmap]
rs7035801	0.82[CHB][hapmap]
rs7038053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7038333	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7042768	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][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	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2762797	chr9:15282415-15297028	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv969751	chr9:15287487-15294727	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13300981	GPR183	trans	lymphoblastoid	seeQTL
rs13300981	TCF7	trans	lymphoblastoid	seeQTL
rs13300981	IL18R1	trans	lymphoblastoid	seeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15254200-15295600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr9:15277600-15296800	Weak transcription	Gastric	stomach
3	chr9:15278000-15295200	Weak transcription	Pancreas	Pancrea
4	chr9:15287000-15294200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:15288600-15294200	Weak transcription	HepG2	liver
7	chr9:15288800-15294800	Weak transcription	Lung	lung
8	chr9:15289200-15295400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:15290800-15294200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:15291200-15294200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:15291200-15296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:15291600-15294200	Weak transcription	Fetal Brain Male	brain
16	chr9:15292000-15294200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:15292200-15294600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:15292200-15296000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:15292200-15296800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:15292600-15295800	Enhancers	HMEC	breast
21	chr9:15292600-15296000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr9:15293000-15294400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:15293000-15295800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr9:15293000-15295800	Enhancers	NHEK	skin
25	chr9:15293000-15296000	Enhancers	Thymus	Thymus
26	chr9:15293200-15294800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr9:15293200-15295600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:15293200-15295600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:15293200-15296000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:15293200-15296000	Enhancers	Fetal Intestine Small	intestine
31	chr9:15293400-15294200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:15293400-15294800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr9:15293400-15294800	Enhancers	Aorta	Aorta
34	chr9:15293400-15295000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:15293400-15295400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:15293400-15295600	Enhancers	NHLF	lung
37	chr9:15293400-15295600	Enhancers	Osteobl	bone
38	chr9:15293400-15295800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr9:15293400-15295800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:15293400-15295800	Enhancers	Fetal Thymus	thymus
41	chr9:15293400-15295800	Enhancers	Right Atrium	heart
42	chr9:15293400-15295800	Enhancers	HSMM	muscle
43	chr9:15293400-15296000	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:15293400-15296400	Enhancers	Fetal Intestine Large	intestine
45	chr9:15293600-15294200	Enhancers	Primary hematopoietic stem cells	blood
46	chr9:15293600-15294200	Active TSS	Colon Smooth Muscle	Colon
47	chr9:15293600-15294400	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr9:15293600-15294400	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr9:15293600-15294400	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr9:15293600-15294600	Flanking Active TSS	Fetal Kidney	kidney

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