Variant report

Variant	rs60629714
Chromosome Location	chr9:95889160-95889161
allele	C/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	HEY1	chr9:95889004-95889667	HepG2	liver:	n/a	n/a
2	MAX	chr9:95889005-95889351	NB4	blood:	n/a	chr9:95889261-95889271
3	HDAC2	chr9:95889075-95889497	HepG2	liver:	n/a	n/a
4	CREB1	chr9:95889024-95889659	HepG2	liver:	n/a	n/a
5	YY1	chr9:95889118-95889607	HepG2	liver:	n/a	n/a
6	POLR2A	chr9:95889085-95889586	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:95889141-95889602	HepG2	liver:	n/a	n/a
8	MYBL2	chr9:95889061-95889557	HepG2	liver:	n/a	n/a
9	HNF4G	chr9:95889120-95889547	HepG2	liver:	n/a	n/a
10	MYC	chr9:95889137-95889553	HepG2	liver:	n/a	chr9:95889401-95889411 chr9:95889261-95889271
11	MAZ	chr9:95889030-95889562	HepG2	liver:	n/a	chr9:95889401-95889411 chr9:95889261-95889271
12	EP300	chr9:95889070-95889526	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr9:95889151-95889336	HepG2	liver:	n/a	n/a
14	POLR2A	chr9:95888966-95889549	HepG2	liver:	n/a	n/a
15	HNF4G	chr9:95889159-95889675	HepG2	liver:	n/a	n/a
16	HNF4A	chr9:95889137-95889687	HepG2	liver:	n/a	n/a
17	POLR2A	chr9:95889004-95889817	HL-60	blood:	n/a	n/a
18	SMC3	chr9:95889149-95889211	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:95889133-95889825	HepG2	liver:	n/a	n/a
20	CREB1	chr9:95888949-95889702	HepG2	liver:	n/a	n/a
21	EGR1	chr9:95889086-95889631	MCF-7	breast:	n/a	chr9:95889323-95889333 chr9:95889262-95889272 chr9:95889321-95889334
22	EGR1	chr9:95888985-95889622	MCF-7	breast:	n/a	chr9:95889323-95889333 chr9:95889024-95889037 chr9:95889262-95889272 chr9:95889024-95889034 chr9:95889321-95889334
23	MYBL2	chr9:95889031-95889612	HepG2	liver:	n/a	n/a
24	HEY1	chr9:95889087-95889620	HepG2	liver:	n/a	n/a
25	EGR1	chr9:95889087-95889534	ECC-1	luminal epithelium:	n/a	chr9:95889323-95889333 chr9:95889262-95889272 chr9:95889321-95889334
26	GABPA	chr9:95889120-95889483	HepG2	liver:	n/a	n/a
27	POLR2A	chr9:95889008-95889684	HepG2	liver:	n/a	n/a
28	EGR1	chr9:95889156-95889426	K562	blood:	n/a	chr9:95889323-95889333 chr9:95889262-95889272 chr9:95889321-95889334
29	TAF1	chr9:95889106-95889613	HepG2	liver:	n/a	n/a
30	HNF4A	chr9:95889110-95889532	HepG2	liver:	n/a	n/a
31	EP300	chr9:95889053-95889601	HepG2	liver:	n/a	n/a
32	GABPA	chr9:95889132-95889498	HepG2	liver:	n/a	n/a
33	CEBPD	chr9:95889074-95889520	HepG2	liver:	n/a	n/a
34	POLR2A	chr9:95888633-95889725	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95857275..95859572-chr9:95888374..95892185,3	MCF-7	breast:
2	chr9:95889078..95891579-chr9:95915235..95918056,2	MCF-7	breast:
3	chr9:95856977..95859126-chr9:95888088..95890598,2	MCF-7	breast:

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

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10992645	0.97[ASN][1000 genomes]
rs12235416	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12237655	0.97[ASN][1000 genomes]
rs12238760	0.96[ASN][1000 genomes]
rs7018885	0.86[ASN][1000 genomes]
rs7032525	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7033638	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72618189	0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60629714	NINJ1	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 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	chr9:95877000-95889200	Weak transcription	Fetal Brain Female	brain
5	chr9:95882800-95889200	Weak transcription	HSMM	muscle
6	chr9:95882800-95889200	Weak transcription	NH-A	brain
7	chr9:95883000-95894600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:95883000-95895000	Weak transcription	HSMMtube	muscle
9	chr9:95883000-95895000	Weak transcription	K562	blood
10	chr9:95884200-95889200	Strong transcription	Gastric	stomach
11	chr9:95885000-95895400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:95886000-95890600	Enhancers	Fetal Thymus	thymus
13	chr9:95886600-95889400	Weak transcription	GM12878-XiMat	blood
14	chr9:95886800-95895400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr9:95887200-95891200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr9:95887400-95890400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:95887400-95890800	Weak transcription	A549	lung
18	chr9:95887400-95891600	Weak transcription	Ovary	ovary
19	chr9:95887400-95893600	Weak transcription	NHLF	lung
20	chr9:95887600-95889200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:95887600-95890800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr9:95887600-95894800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr9:95887800-95893400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:95887800-95894000	Weak transcription	Brain Germinal Matrix	brain
25	chr9:95888000-95890400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:95888000-95890800	Enhancers	Primary T cells from cord blood	blood
27	chr9:95888000-95890800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:95888000-95891600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:95888200-95889200	Genic enhancers	Fetal Intestine Large	intestine
30	chr9:95888200-95889200	Enhancers	Thymus	Thymus
31	chr9:95888200-95889400	Weak transcription	Pancreas	Pancrea
32	chr9:95888200-95890000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:95888200-95890600	Enhancers	Primary hematopoietic stem cells	blood
34	chr9:95888200-95890600	Weak transcription	Brain Angular Gyrus	brain
35	chr9:95888200-95891000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:95888200-95892200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr9:95888200-95893400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:95888200-95893400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr9:95888200-95894600	Weak transcription	Osteobl	bone
40	chr9:95888200-95895000	Enhancers	Esophagus	oesophagus
41	chr9:95888400-95889200	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr9:95888400-95889200	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr9:95888400-95889600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:95888400-95890200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:95888400-95890400	Enhancers	Brain Hippocampus Middle	brain
46	chr9:95888400-95890400	Genic enhancers	Fetal Intestine Small	intestine
47	chr9:95888400-95891000	Genic enhancers	Liver	Liver
48	chr9:95888400-95894200	Weak transcription	Hela-S3	cervix
49	chr9:95888400-95894800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr9:95888400-95895000	Enhancers	HUVEC	blood vessel

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