Variant report

Variant	rs60465887
Chromosome Location	chr9:21809992-21809993
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	BCL11A	chr9:21809820-21810259	GM12878	blood:	n/a	n/a
2	MTA3	chr9:21809772-21810199	GM12878	blood:	n/a	n/a
3	IRF4	chr9:21809758-21810267	GM12878	blood:	n/a	n/a
4	CEBPB	chr9:21809751-21810356	GM12878	blood:	n/a	n/a
5	NFATC1	chr9:21809735-21810283	GM12878	blood:	n/a	n/a
6	CEBPB	chr9:21809975-21810230	Hela-S3	cervix:	n/a	n/a
7	ATF2	chr9:21809791-21810234	GM12878	blood:	n/a	n/a
8	EP300	chr9:21809911-21810093	GM12878	blood:	n/a	chr9:21810032-21810046
9	BATF	chr9:21809783-21810274	GM12878	blood:	n/a	n/a
10	NFATC1	chr9:21809808-21810280	GM12878	blood:	n/a	n/a
11	RUNX3	chr9:21809789-21810252	GM12878	blood:	n/a	n/a
12	RUNX3	chr9:21809725-21810305	GM12878	blood:	n/a	n/a
13	MTA3	chr9:21809771-21810319	GM12878	blood:	n/a	n/a
14	CEBPB	chr9:21809891-21810217	IMR90	lung:	n/a	n/a
15	NFIC	chr9:21809795-21810237	GM12878	blood:	n/a	n/a
16	BCL3	chr9:21809834-21810198	GM12878	blood:	n/a	n/a
17	POLR2A	chr9:21809656-21810022	HCT-116	colon:	n/a	n/a
18	BATF	chr9:21809849-21810198	GM12878	blood:	n/a	n/a
19	ATF2	chr9:21809644-21810268	GM12878	blood:	n/a	n/a
20	STAT5A	chr9:21809845-21810186	GM12878	blood:	n/a	n/a
21	PML	chr9:21809767-21810273	GM12878	blood:	n/a	n/a
22	MEF2A	chr9:21809721-21810298	GM12878	blood:	n/a	chr9:21809909-21809920 chr9:21809908-21809923
23	FOXM1	chr9:21809688-21810274	GM12878	blood:	n/a	n/a
24	CREB1	chr9:21809826-21810354	GM12878	blood:	n/a	n/a
25	FOXM1	chr9:21809695-21810320	GM12878	blood:	n/a	n/a
26	NFIC	chr9:21809628-21810280	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000266732	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1440994	1.00[EUR][1000 genomes]
rs58005508	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59397155	1.00[EUR][1000 genomes]
rs59828051	1.00[EUR][1000 genomes]
rs7027003	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7041147	1.00[EUR][1000 genomes]
rs7041757	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73429337	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73429360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73429364	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73649991	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1026981	chr9:21748202-21811697	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
3	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21810800	Weak transcription	Right Ventricle	heart
2	chr9:21804000-21814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr9:21804200-21810800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr9:21804200-21813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:21804200-21813200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr9:21804400-21813200	Weak transcription	Colonic Mucosa	Colon
9	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
10	chr9:21804600-21810400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:21804800-21813600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr9:21805000-21810800	Weak transcription	Brain Anterior Caudate	brain
13	chr9:21805000-21811200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:21805000-21812000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:21805000-21813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
17	chr9:21805200-21810000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr9:21805200-21810800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:21805200-21810800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:21805200-21812800	Strong transcription	Fetal Stomach	stomach
21	chr9:21805200-21813200	Weak transcription	Psoas Muscle	Psoas
22	chr9:21805200-21813400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr9:21805400-21812600	Strong transcription	Fetal Intestine Large	intestine
24	chr9:21805600-21810200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:21805800-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:21805800-21813200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:21806000-21812400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:21806000-21812600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:21806000-21817600	Genic enhancers	HMEC	breast
30	chr9:21806200-21810000	Weak transcription	Fetal Brain Female	brain
31	chr9:21806200-21813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr9:21806400-21812200	Strong transcription	Fetal Intestine Small	intestine
33	chr9:21806400-21812400	Strong transcription	HepG2	liver
34	chr9:21806400-21812800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:21806400-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr9:21806400-21813200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr9:21806600-21810800	Weak transcription	Pancreas	Pancrea
39	chr9:21806600-21812200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr9:21806600-21812400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:21806600-21815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr9:21806800-21810800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:21806800-21810800	Weak transcription	Lung	lung
45	chr9:21806800-21811600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr9:21806800-21812000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:21806800-21812000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr9:21806800-21812800	Strong transcription	Primary T cells from cord blood	blood
49	chr9:21806800-21813200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr9:21806800-21815800	Weak transcription	Brain Germinal Matrix	brain

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