Variant report

Variant	rs2897119
Chromosome Location	chr20:23623261-23623262
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	CEBPB	chr20:23622936-23623311	HepG2	liver:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
2	FOS	chr20:23623038-23623393	MCF10A-Er-Src	breast:	n/a	chr20:23623300-23623310 chr20:23623301-23623309 chr20:23623299-23623311 chr20:23623302-23623313 chr20:23623300-23623310
3	POLR2A	chr20:23622960-23623489	HUVEC	blood vessel:	n/a	n/a
4	RCOR1	chr20:23622864-23623663	IMR90	lung:	n/a	n/a
5	PBX3	chr20:23622909-23623504	SK-N-SH	brain:	n/a	n/a
6	FOS	chr20:23623168-23623367	MCF10A-Er-Src	breast:	n/a	chr20:23623300-23623310 chr20:23623301-23623309 chr20:23623299-23623311 chr20:23623302-23623313 chr20:23623300-23623310
7	CTCF	chr20:23623240-23623390	HMF	breast:	n/a	n/a
8	CEBPB	chr20:23622974-23623316	HepG2	liver:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
9	TCF12	chr20:23622773-23623557	SK-N-SH	brain:	n/a	n/a
10	FOS	chr20:23622910-23623540	HUVEC	blood vessel:	n/a	chr20:23623300-23623310 chr20:23623301-23623309 chr20:23623299-23623311 chr20:23623302-23623313 chr20:23623300-23623310
11	POLR2A	chr20:23622982-23623385	HUVEC	blood vessel:	n/a	n/a
12	TCF12	chr20:23622761-23623663	SK-N-SH	brain:	n/a	n/a
13	CEBPB	chr20:23622958-23623482	IMR90	lung:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
14	TCF7L2	chr20:23623047-23623438	HepG2	liver:	n/a	chr20:23623300-23623309
15	CEBPB	chr20:23622988-23623362	MCF-7	breast:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
16	CTCF	chr20:23623160-23623310	RPTEC	kidney:	n/a	n/a
17	CEBPB	chr20:23623082-23623292	H1-hESC	embryonic stem cell:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
18	CEBPB	chr20:23622959-23623311	HepG2	liver:	n/a	chr20:23623134-23623147 chr20:23623135-23623146
19	FOSL2	chr20:23622841-23623593	SK-N-SH	brain:	n/a	chr20:23623300-23623310 chr20:23623301-23623309 chr20:23623299-23623311 chr20:23623302-23623313 chr20:23623300-23623310
20	GABPA	chr20:23622964-23623494	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23615698..23619686-chr20:23620113..23624171,4	MCF-7	breast:
2	chr20:23616967..23620200-chr20:23620235..23623406,7	MCF-7	breast:

Variant related genes	Relation type
CST3	TF binding region
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1064039	0.80[EUR][1000 genomes]
rs13041070	0.81[EUR][1000 genomes]
rs2016161	0.81[EUR][1000 genomes]
rs2254635	0.88[EUR][1000 genomes]
rs2405367	0.88[EUR][1000 genomes]
rs2424582	0.89[EUR][1000 genomes]
rs34746357	0.82[EUR][1000 genomes]
rs34897231	0.82[EUR][1000 genomes]
rs35488434	0.82[EUR][1000 genomes]
rs35610040	0.81[EUR][1000 genomes]
rs35966482	0.82[EUR][1000 genomes]
rs3761280	0.82[EUR][1000 genomes]
rs3761281	0.82[EUR][1000 genomes]
rs3787498	0.81[EUR][1000 genomes]
rs3787499	0.80[EUR][1000 genomes]
rs3827141	0.81[EUR][1000 genomes]
rs3827143	0.82[EUR][1000 genomes]
rs5030707	0.83[EUR][1000 genomes]
rs6114208	0.83[EUR][1000 genomes]
rs6114209	0.83[EUR][1000 genomes]
rs67567111	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2897119	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23624800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:23618600-23626000	Weak transcription	Gastric	stomach
3	chr20:23618800-23625200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr20:23620000-23625000	Enhancers	Fetal Thymus	thymus
7	chr20:23620200-23623600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr20:23620800-23623400	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr20:23620800-23624400	Enhancers	Fetal Muscle Leg	muscle
10	chr20:23621200-23623400	Enhancers	Ovary	ovary
11	chr20:23621200-23623600	Enhancers	GM12878-XiMat	blood
12	chr20:23621200-23625200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:23621400-23623600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr20:23621400-23624800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr20:23621400-23625000	Enhancers	Adipose Nuclei	Adipose
16	chr20:23621600-23623600	Enhancers	Brain Hippocampus Middle	brain
17	chr20:23621600-23623800	Enhancers	HSMM	muscle
18	chr20:23621800-23623600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr20:23621800-23623800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr20:23621800-23624600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr20:23622000-23623600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr20:23622000-23623600	Enhancers	HSMMtube	muscle
23	chr20:23622000-23623800	Enhancers	HUVEC	blood vessel
24	chr20:23622000-23624200	Weak transcription	Primary B cells from cord blood	blood
25	chr20:23622000-23625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:23622200-23623800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:23622200-23623800	Enhancers	Muscle Satellite Cultured Cells	--
28	chr20:23622200-23624800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
30	chr20:23622400-23623400	Enhancers	Fetal Muscle Trunk	muscle
31	chr20:23622400-23623800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:23622400-23623800	Enhancers	Osteobl	bone
33	chr20:23622400-23624000	Enhancers	NHDF-Ad	bronchial
34	chr20:23622400-23624200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr20:23622400-23624400	Enhancers	NHLF	lung
36	chr20:23622600-23623400	Enhancers	Brain Substantia Nigra	brain
37	chr20:23622600-23623600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:23622600-23623600	Enhancers	Brain Anterior Caudate	brain
39	chr20:23622600-23623600	Enhancers	Colon Smooth Muscle	Colon
40	chr20:23622800-23623400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr20:23622800-23623400	Enhancers	Colonic Mucosa	Colon
42	chr20:23622800-23623600	Weak transcription	Psoas Muscle	Psoas
43	chr20:23622800-23623800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:23622800-23624000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr20:23622800-23625400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr20:23622800-23625400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
48	chr20:23623000-23623400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr20:23623000-23623400	Enhancers	Placenta Amnion	Placenta Amnion
50	chr20:23623000-23623400	Enhancers	Skeletal Muscle Male	skeletal muscle

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