Variant report

Variant	rs13284407
Chromosome Location	chr9:95888521-95888522
allele	G/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	POLR2A	chr9:95888517-95888918	GM12878	blood:	n/a	n/a
2	ELF1	chr9:95888353-95888880	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95857275..95859572-chr9:95888374..95892185,3	MCF-7	breast:
2	chr9:95856977..95859126-chr9:95888088..95890598,2	MCF-7	breast:

Variant related genes	Relation type
NINJ1	TF binding region
ENSG00000223446	Chromatin interaction
ENSG00000165233	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1127857	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004134	1.00[ASN][1000 genomes]
rs12005054	1.00[ASN][1000 genomes]
rs13284544	1.00[ASN][1000 genomes]
rs13284731	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13285019	1.00[ASN][1000 genomes]
rs13285107	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286331	1.00[ASN][1000 genomes]
rs13294417	1.00[ASN][1000 genomes]
rs13297094	1.00[ASN][1000 genomes]
rs13298119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13299270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300450	1.00[ASN][1000 genomes]
rs34297115	1.00[ASN][1000 genomes]
rs34476050	1.00[ASN][1000 genomes]
rs35476990	1.00[ASN][1000 genomes]
rs36034699	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743906	1.00[ASN][1000 genomes]
rs7033638	0.81[EUR][1000 genomes]
rs7035004	1.00[ASN][1000 genomes]
rs7037142	1.00[ASN][1000 genomes]
rs7871317	1.00[ASN][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	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv893579	chr9:95855100-95923091	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv893581	chr9:95872216-95930334	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer 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 target site	17 gene(s)	inside rSNPs	diseases
8	nsv614879	chr9:95883363-95897564	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13284407	NINJ1	cis	Artery Tibial	GTEx
rs13284407	NINJ1	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95859600-95889400	Weak transcription	Fetal Kidney	kidney
2	chr9:95870000-95895400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:95871000-95894200	Weak transcription	Dnd41	blood
4	chr9:95873400-95888800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr9:95877000-95889200	Weak transcription	Fetal Brain Female	brain
6	chr9:95877200-95888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:95879200-95888600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr9:95879200-95889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:95882600-95888600	Weak transcription	Fetal Lung	lung
10	chr9:95882600-95888600	Weak transcription	Right Atrium	heart
11	chr9:95882800-95889000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:95882800-95889200	Weak transcription	HSMM	muscle
13	chr9:95882800-95889200	Weak transcription	NH-A	brain
14	chr9:95883000-95889000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:95883000-95894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
17	chr9:95883000-95895000	Weak transcription	K562	blood
18	chr9:95883200-95888600	Strong transcription	Fetal Stomach	stomach
19	chr9:95883200-95888600	Strong transcription	Lung	lung
20	chr9:95883200-95888800	Weak transcription	Psoas Muscle	Psoas
21	chr9:95883400-95888600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:95883600-95888600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:95883600-95888800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:95883600-95888800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr9:95883800-95888800	Strong transcription	Aorta	Aorta
26	chr9:95884200-95888600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:95884200-95889200	Strong transcription	Gastric	stomach
28	chr9:95885000-95895400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:95885200-95888600	Strong transcription	Adipose Nuclei	Adipose
30	chr9:95885200-95888800	Weak transcription	Primary B cells from cord blood	blood
31	chr9:95885800-95888600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:95885800-95888600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:95885800-95888600	Strong transcription	Brain Substantia Nigra	brain
34	chr9:95886000-95888600	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr9:95886000-95890600	Enhancers	Fetal Thymus	thymus
36	chr9:95886200-95888600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:95886200-95888800	Weak transcription	Fetal Brain Male	brain
38	chr9:95886200-95889000	Genic enhancers	Spleen	Spleen
39	chr9:95886400-95888600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:95886400-95888800	Weak transcription	Fetal Heart	heart
41	chr9:95886600-95888600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr9:95886600-95889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr9:95886600-95889400	Weak transcription	GM12878-XiMat	blood
44	chr9:95886800-95888800	Weak transcription	HMEC	breast
45	chr9:95886800-95895400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr9:95887200-95888800	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr9:95887200-95891200	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr9:95887400-95888600	Weak transcription	Right Ventricle	heart
49	chr9:95887400-95890400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr9:95887400-95890800	Weak transcription	A549	lung

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