Variant report

Variant	rs13298119
Chromosome Location	chr9:95887154-95887155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10117910	1.00[CHB][hapmap]
rs10992583	1.00[CHB][hapmap]
rs1127851	1.00[CEU][hapmap]
rs1127857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12004134	1.00[ASN][1000 genomes]
rs12005054	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12235416	0.87[TSI][hapmap]
rs13284407	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284544	1.00[ASN][1000 genomes]
rs13284731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.80[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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13286331	1.00[ASN][1000 genomes]
rs13287304	1.00[CHB][hapmap]
rs13294417	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13297094	1.00[ASN][1000 genomes]
rs13299270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13300450	1.00[ASN][1000 genomes]
rs2275848	1.00[CEU][hapmap];0.83[MKK][hapmap]
rs34297115	1.00[ASN][1000 genomes]
rs34476050	1.00[ASN][1000 genomes]
rs35476990	1.00[ASN][1000 genomes]
rs36034699	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743906	1.00[ASN][1000 genomes]
rs7024692	1.00[CHB][hapmap]
rs7033638	0.81[EUR][1000 genomes]
rs7035004	1.00[ASN][1000 genomes]
rs7037142	1.00[ASN][1000 genomes]
rs7048701	1.00[CHB][hapmap]
rs7852416	1.00[CHB][hapmap]
rs7854887	1.00[CHB][hapmap]
rs7855476	1.00[CHB][hapmap]
rs7871317	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13298119	NINJ1	cis	Thyroid	GTEx
rs13298119	NINJ1	cis	Artery Tibial	GTEx
rs13298119	NOL8	cis	cerebellum	SCAN
rs13298119	NINJ1	cis	cerebellum	SCAN

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	chr9:95882400-95888200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:95882600-95887200	Weak transcription	Thymus	Thymus
11	chr9:95882600-95888600	Weak transcription	Fetal Lung	lung
12	chr9:95882600-95888600	Weak transcription	Right Atrium	heart
13	chr9:95882800-95889000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:95882800-95889200	Weak transcription	HSMM	muscle
15	chr9:95882800-95889200	Weak transcription	NH-A	brain
16	chr9:95883000-95887400	Weak transcription	Stomach Mucosa	stomach
17	chr9:95883000-95887400	Weak transcription	Hela-S3	cervix
18	chr9:95883000-95887600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr9:95883000-95887600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:95883000-95888000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:95883000-95888200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr9:95883000-95888200	Strong transcription	Fetal Intestine Large	intestine
23	chr9:95883000-95888400	Strong transcription	Fetal Intestine Small	intestine
24	chr9:95883000-95888400	Weak transcription	HUVEC	blood vessel
25	chr9:95883000-95889000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr9:95883000-95894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
28	chr9:95883000-95895000	Weak transcription	K562	blood
29	chr9:95883200-95888000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:95883200-95888600	Strong transcription	Fetal Stomach	stomach
31	chr9:95883200-95888600	Strong transcription	Lung	lung
32	chr9:95883200-95888800	Weak transcription	Psoas Muscle	Psoas
33	chr9:95883400-95887600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:95883400-95888000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:95883400-95888000	Strong transcription	Colon Smooth Muscle	Colon
36	chr9:95883400-95888400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:95883400-95888600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:95883600-95887400	Strong transcription	NHLF	lung
39	chr9:95883600-95887800	Strong transcription	Left Ventricle	heart
40	chr9:95883600-95888200	Strong transcription	Brain Angular Gyrus	brain
41	chr9:95883600-95888200	Strong transcription	Pancreas	Pancrea
42	chr9:95883600-95888200	Strong transcription	HepG2	liver
43	chr9:95883600-95888400	Strong transcription	Liver	Liver
44	chr9:95883600-95888600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:95883600-95888800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:95883600-95888800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
47	chr9:95883800-95887200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr9:95883800-95887600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:95883800-95887600	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr9:95883800-95888000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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