Variant report

Variant	rs12337469
Chromosome Location	chr9:95898655-95898656
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	FOXA1	chr9:95898419-95898725	HepG2	liver:	n/a	chr9:95898587-95898602
2	POLR2A	chr9:95898402-95898655	HepG2	liver:	n/a	n/a
3	FOXA2	chr9:95898391-95898691	HepG2	liver:	n/a	n/a
4	ZNF384	chr9:95898492-95898785	K562	blood:	n/a	n/a
5	FOXA1	chr9:95898362-95898685	T-47D	breast:	n/a	chr9:95898587-95898602
6	FOXA1	chr9:95898421-95898710	T-47D	breast:	n/a	chr9:95898587-95898602
7	SP1	chr9:95898385-95898720	A549	lung:	n/a	n/a
8	FOXA1	chr9:95898308-95898708	HepG2	liver:	n/a	chr9:95898587-95898602
9	FOXA2	chr9:95898278-95898743	A549	lung:	n/a	n/a
10	TBP	chr9:95898507-95898661	HepG2	liver:	n/a	n/a
11	FOXA1	chr9:95898499-95898681	ECC-1	luminal epithelium:	n/a	chr9:95898587-95898602
12	FOXA1	chr9:95898334-95898703	HepG2	liver:	n/a	chr9:95898587-95898602
13	FOXA2	chr9:95898409-95898900	A549	lung:	n/a	n/a
14	FOXA1	chr9:95898354-95898704	HepG2	liver:	n/a	chr9:95898587-95898602
15	FOXP2	chr9:95898359-95898657	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:95895042..95899051-chr9:95945154..95949540,5	MCF-7	breast:
2	chr9:95893768..95895658-chr9:95897377..95900133,3	K562	blood:
3	chr9:95856253..95862485-chr9:95892353..95899486,12	MCF-7	breast:
4	chr9:95897165..95898764-chr9:95898859..95901008,2	K562	blood:
5	chr9:95855662..95862507-chr9:95894736..95899302,16	MCF-7	breast:

Variant related genes	Relation type
NINJ1	TF binding region
ENSG00000165238	Chromatin interaction
ENSG00000165233	Chromatin interaction
ENSG00000223446	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12342200	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025554	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73524733	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7867389	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7867526	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95896000-95899200	Enhancers	Fetal Brain Male	brain
2	chr9:95897200-95898800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:95897200-95899200	Enhancers	Brain Anterior Caudate	brain
4	chr9:95897200-95899200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr9:95897200-95899200	Enhancers	Pancreas	Pancrea
6	chr9:95897200-95899400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:95897200-95899400	Enhancers	Placenta	Placenta
8	chr9:95897200-95900200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:95897200-95900400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:95897200-95900400	Enhancers	Esophagus	oesophagus
11	chr9:95897200-95900400	Enhancers	Fetal Muscle Leg	muscle
12	chr9:95897200-95901000	Enhancers	Brain Cingulate Gyrus	brain
13	chr9:95897200-95902400	Enhancers	Primary B cells from peripheral blood	blood
14	chr9:95897200-95906200	Weak transcription	Right Atrium	heart
15	chr9:95897400-95899000	Enhancers	Brain Hippocampus Middle	brain
16	chr9:95897400-95900400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:95897400-95900800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr9:95897400-95901000	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr9:95897400-95906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:95897600-95899600	Weak transcription	HMEC	breast
21	chr9:95897600-95900000	Weak transcription	Fetal Intestine Small	intestine
22	chr9:95897600-95900200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:95897600-95904600	Weak transcription	Psoas Muscle	Psoas
24	chr9:95897600-95906000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:95897600-95906200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr9:95897800-95898800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:95897800-95899000	Weak transcription	Fetal Thymus	thymus
28	chr9:95897800-95900200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:95897800-95900400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr9:95897800-95900400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:95897800-95902600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:95897800-95903000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr9:95897800-95903000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:95897800-95903000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:95898000-95899000	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr9:95898000-95899000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr9:95898000-95899200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr9:95898000-95900000	Weak transcription	Primary B cells from cord blood	blood
39	chr9:95898000-95900200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:95898000-95902400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr9:95898000-95904200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr9:95898200-95898800	Flanking Active TSS	Colon Smooth Muscle	Colon
43	chr9:95898200-95898800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr9:95898200-95898800	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr9:95898200-95899200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:95898400-95899200	Enhancers	Lung	lung
47	chr9:95898400-95899200	Enhancers	Spleen	Spleen
48	chr9:95898400-95899600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:95898400-95899800	Enhancers	Gastric	stomach
50	chr9:95898600-95898800	Bivalent/Poised TSS	NHEK	skin

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