Variant report

Variant	rs13297121
Chromosome Location	chr9:71994882-71994883
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	chr9:71649254..71651788-chr9:71993811..71996699,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165060	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1034238	0.84[EUR][1000 genomes]
rs11139245	0.81[JPT][hapmap]
rs11139246	0.81[JPT][hapmap]
rs12003507	0.84[ASN][1000 genomes]
rs12551899	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13284247	0.84[ASN][1000 genomes]
rs13284677	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13285975	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13290881	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13291679	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs13296504	0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13298045	0.82[ASN][1000 genomes]
rs13300133	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17412941	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.85[ASN][1000 genomes]
rs1855529	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs2253778	0.86[JPT][hapmap]
rs34133536	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34295676	0.85[ASN][1000 genomes]
rs34672585	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4307408	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4351475	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4554547	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.85[ASN][1000 genomes]
rs4744885	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[ASN][1000 genomes]
rs4744893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60284429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028920	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7033124	0.85[ASN][1000 genomes]
rs7853058	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7855000	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7867609	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867366	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv893428	chr9:71926658-72027641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13297121	NCOR2	trans	brain	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71979000-72001800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:71983400-72001800	Weak transcription	Brain Anterior Caudate	brain
3	chr9:71985400-72006600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:71986600-72002600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:71988800-71998600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr9:71989000-72002800	Weak transcription	Brain Substantia Nigra	brain
7	chr9:71989600-71997000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:71990600-72000200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:71991800-72012200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:71992000-71995800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:71992000-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:71992000-72009800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:71992200-71997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:71992200-72001800	Weak transcription	Adipose Nuclei	Adipose
15	chr9:71992400-71999400	Weak transcription	Brain Angular Gyrus	brain
16	chr9:71992400-72001800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:71992600-71995200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:71992600-71996000	Weak transcription	Right Atrium	heart
19	chr9:71992600-72000800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:71992600-72006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:71992600-72006600	Weak transcription	Esophagus	oesophagus
22	chr9:71992800-71997200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:71992800-71997400	Enhancers	Fetal Muscle Leg	muscle
24	chr9:71992800-71998200	Weak transcription	Ovary	ovary
25	chr9:71992800-71998400	Weak transcription	Fetal Stomach	stomach
26	chr9:71992800-72000200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:71992800-72001400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:71993000-71997000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr9:71993000-72006600	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:71993600-71996000	Enhancers	HUVEC	blood vessel
31	chr9:71993600-71997200	Enhancers	Stomach Smooth Muscle	stomach
32	chr9:71993800-71995000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:71993800-71995400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:71993800-71996200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:71994000-71995200	Flanking Active TSS	HSMMtube	muscle
36	chr9:71994000-71995800	Enhancers	Placenta	Placenta
37	chr9:71994000-71996000	Enhancers	Fetal Heart	heart
38	chr9:71994000-71997400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:71994000-71997400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:71994200-71995000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr9:71994200-71995000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:71994200-71995000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:71994200-71995000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:71994200-71995000	Enhancers	Aorta	Aorta
45	chr9:71994200-71995000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr9:71994200-71995000	Enhancers	Stomach Mucosa	stomach
47	chr9:71994200-71995000	Flanking Active TSS	HSMM	muscle
48	chr9:71994200-71995000	Enhancers	NHDF-Ad	bronchial
49	chr9:71994200-71995000	Flanking Active TSS	Osteobl	bone
50	chr9:71994200-71995200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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