Variant report

Variant	rs4743894
Chromosome Location	chr9:95905552-95905553
allele	A/C
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	HNF4A	chr9:95905349-95905718	HepG2	liver:	n/a	chr9:95905562-95905574 chr9:95905559-95905577 chr9:95905560-95905575
2	ZBTB7A	chr9:95905421-95905672	HepG2	liver:	n/a	n/a
3	HNF4A	chr9:95905455-95905661	HepG2	liver:	n/a	chr9:95905562-95905574 chr9:95905559-95905577 chr9:95905560-95905575
4	SP1	chr9:95905358-95905742	HepG2	liver:	n/a	n/a
5	ZBTB7A	chr9:95905451-95905596	HepG2	liver:	n/a	n/a
6	RXRA	chr9:95905401-95905724	HepG2	liver:	n/a	chr9:95905534-95905547 chr9:95905562-95905576
7	HNF4G	chr9:95905416-95905683	HepG2	liver:	n/a	chr9:95905562-95905574 chr9:95905559-95905577

No.	Distal block	Cell Line	Cell type
1	chr9:95871383..95871951-chr9:95904635..95905632,2	MCF-7	breast:
2	chr9:95905509..95907695-chr9:96212278..96215177,2	MCF-7	breast:
3	chr9:95904775..95906435-chr9:96074379..96077038,2	MCF-7	breast:
4	chr9:95899271..95900949-chr9:95904032..95906228,2	K562	blood:
5	chr9:95890205..95893165-chr9:95905253..95907697,2	MCF-7	breast:
6	chr9:95894166..95899165-chr9:95902753..95906319,6	K562	blood:
7	chr9:95900207..95903204-chr9:95903529..95906753,3	MCF-7	breast:
8	chr9:95902681..95906471-chr9:95910340..95913380,3	MCF-7	breast:
9	chr9:95857596..95859444-chr9:95904175..95906038,2	MCF-7	breast:
10	chr9:95902234..95904714-chr9:95904881..95906837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203364	TF binding region
ENSG00000165233	Chromatin interaction
ENSG00000048828	Chromatin interaction
ENSG00000131669	Chromatin interaction
ENSG00000188938	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10761195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821075	0.80[CHB][hapmap]
rs10821076	0.80[CHB][hapmap];0.81[CHD][hapmap]
rs10992653	0.97[ASN][1000 genomes]
rs1833035	0.98[ASN][1000 genomes]
rs2398825	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2398827	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743896	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744181	0.81[AFR][1000 genomes];0.97[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	nsv824983	chr9:95902154-95978408	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4743894	NINJ1	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95897200-95906200	Weak transcription	Right Atrium	heart
2	chr9:95897400-95906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:95897600-95906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:95897600-95906200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr9:95898600-95905600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:95898600-95906200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr9:95899000-95906200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr9:95899400-95906200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr9:95899600-95907200	Enhancers	Fetal Thymus	thymus
10	chr9:95899800-95907400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr9:95899800-95922200	Weak transcription	Gastric	stomach
12	chr9:95901000-95905600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr9:95901000-95906000	Weak transcription	GM12878-XiMat	blood
14	chr9:95901000-95906200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:95901000-95906200	Weak transcription	Primary B cells from cord blood	blood
16	chr9:95901000-95906200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:95901000-95906200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:95901000-95906200	Weak transcription	Spleen	Spleen
19	chr9:95901200-95905800	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:95901600-95907800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:95901800-95906200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr9:95901800-95907400	Enhancers	Primary T cells from cord blood	blood
23	chr9:95902000-95906200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:95902000-95906400	Weak transcription	HSMM	muscle
25	chr9:95902400-95907400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:95902600-95905600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr9:95902600-95905600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:95902800-95906200	Weak transcription	Thymus	Thymus
29	chr9:95903000-95905600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr9:95903000-95907600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:95903400-95906200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:95903600-95906000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr9:95903600-95906200	Weak transcription	HUVEC	blood vessel
34	chr9:95903800-95906000	Weak transcription	Brain Anterior Caudate	brain
35	chr9:95904000-95905600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:95904000-95907200	Enhancers	Fetal Muscle Leg	muscle
37	chr9:95904200-95906200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:95904200-95906400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:95904200-95907000	Enhancers	Fetal Muscle Trunk	muscle
40	chr9:95904200-95907200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr9:95904200-95907200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr9:95904400-95907200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr9:95904600-95905600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:95904600-95906200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:95904600-95906200	Weak transcription	Fetal Brain Female	brain
46	chr9:95904600-95906200	Weak transcription	NHEK	skin
47	chr9:95904600-95906400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:95904800-95905600	Weak transcription	Colonic Mucosa	Colon
49	chr9:95904800-95906200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:95904800-95906200	Weak transcription	Esophagus	oesophagus

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