Variant report

Variant	rs854889
Chromosome Location	chr12:47471037-47471038
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	JUN	chr12:47471023-47471253	HepG2	liver:	n/a	n/a
2	USF1	chr12:47470830-47473507	A549	lung:	n/a	chr12:47473360-47473376 chr12:47473419-47473435
3	SP1	chr12:47470742-47475642	A549	lung:	n/a	chr12:47473708-47473722 chr12:47473736-47473749 chr12:47475085-47475094 chr12:47475083-47475095 chr12:47473915-47473929 chr12:47473912-47473924 chr12:47473913-47473922 chr12:47473787-47473799 chr12:47472827-47472841 chr12:47473912-47473924
4	GATA3	chr12:47470761-47475650	A549	lung:	n/a	chr12:47474494-47474501 chr12:47474492-47474501 chr12:47474492-47474502 chr12:47474494-47474501 chr12:47474483-47474500 chr12:47474487-47474508 chr12:47474494-47474501 chr12:47474489-47474505 chr12:47474451-47474461 chr12:47474902-47474911
5	EP300	chr12:47470956-47472760	A549	lung:	n/a	n/a
6	ATF3	chr12:47470877-47473418	A549	lung:	n/a	n/a
7	EP300	chr12:47470894-47472068	A549	lung:	n/a	n/a
8	TCF12	chr12:47470890-47477595	A549	lung:	n/a	n/a
9	REST	chr12:47470302-47473575	A549	lung:	n/a	chr12:47473473-47473486
10	CTCF	chr12:47470960-47471110	NHDF-neo	bronchial:	n/a	n/a
11	FOSL2	chr12:47470511-47473593	A549	lung:	n/a	chr12:47473368-47473377
12	TAF1	chr12:47470805-47475443	A549	lung:	n/a	n/a
13	BCL3	chr12:47466534-47473485	A549	lung:	n/a	chr12:47473417-47473426 chr12:47473419-47473432
14	SP1	chr12:47470987-47475409	A549	lung:	n/a	chr12:47473708-47473722 chr12:47473736-47473749 chr12:47475085-47475094 chr12:47475083-47475095 chr12:47473915-47473929 chr12:47473912-47473924 chr12:47473913-47473922 chr12:47473787-47473799 chr12:47472827-47472841 chr12:47473912-47473924
15	SIN3AK20	chr12:47470751-47473170	A549	lung:	n/a	n/a
16	POLR2A	chr12:47468540-47475394	A549	lung:	n/a	n/a
17	MAX	chr12:47470868-47475608	A549	lung:	n/a	chr12:47473840-47473850
18	JUND	chr12:47471031-47471380	HepG2	liver:	n/a	n/a
19	SIX5	chr12:47468477-47473570	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:47468454..47471376-chr12:47472696..47475004,3	K562	blood:
2	chr12:47434957..47437374-chr12:47470589..47472763,3	MCF-7	breast:
3	chr12:47463342..47465286-chr12:47468931..47471873,3	K562	blood:
4	chr12:47470140..47471786-chr12:47702328..47704008,2	MCF-7	breast:
5	chr12:47462488..47464842-chr12:47470373..47472579,2	K562	blood:
6	chr12:47470124..47472497-chr12:47479611..47481328,2	K562	blood:
7	chr12:47470563..47472586-chr12:47627507..47630437,2	MCF-7	breast:

Variant related genes	Relation type
PCED1B	TF binding region
ENSG00000139211	Chromatin interaction
ENSG00000179715	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10736030	1.00[YRI][hapmap]
rs10785650	1.00[YRI][hapmap]
rs1101753	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768771	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961460	1.00[YRI][hapmap]
rs854888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854890	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv694	chr12:47460716-47473382	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47460800-47471800	Weak transcription	Fetal Intestine Small	intestine
2	chr12:47462600-47471400	Weak transcription	Lung	lung
3	chr12:47462800-47471200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:47463200-47471400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:47463400-47472400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:47465200-47471200	Weak transcription	Pancreas	Pancrea
7	chr12:47468800-47472400	Weak transcription	HUVEC	blood vessel
8	chr12:47469000-47473200	Transcr. at gene 5' and 3'	A549	lung
9	chr12:47469400-47472600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:47469600-47471800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:47469600-47472000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:47469800-47471200	Weak transcription	Ovary	ovary
13	chr12:47469800-47471200	Active TSS	HSMMtube	muscle
14	chr12:47469800-47472600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:47469800-47472600	Weak transcription	Thymus	Thymus
16	chr12:47469800-47472800	Transcr. at gene 5' and 3'	NHEK	skin
17	chr12:47470000-47471800	Weak transcription	NHLF	lung
18	chr12:47470000-47475000	Active TSS	Colon Smooth Muscle	Colon
19	chr12:47470200-47471200	Strong transcription	HSMM	muscle
20	chr12:47470200-47471400	Weak transcription	Spleen	Spleen
21	chr12:47470400-47471200	Enhancers	Rectal Smooth Muscle	rectum
22	chr12:47470400-47471400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:47470400-47472200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:47470400-47472400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:47470600-47471200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:47470600-47471200	Weak transcription	Fetal Intestine Large	intestine
27	chr12:47470600-47471600	Enhancers	Primary T cells from cord blood	blood
28	chr12:47470600-47472000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr12:47470600-47472600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr12:47470800-47471200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:47470800-47471200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr12:47470800-47471200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:47470800-47472000	Transcr. at gene 5' and 3'	Osteobl	bone
34	chr12:47470800-47475000	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr12:47471000-47471200	Active TSS	Aorta	Aorta
36	chr12:47471000-47471400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr12:47471000-47471400	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr12:47471000-47471400	Flanking Active TSS	HMEC	breast
39	chr12:47471000-47472000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:47471000-47472000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
41	chr12:47471000-47472000	Enhancers	Adipose Nuclei	Adipose
42	chr12:47471000-47472200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:47471000-47472400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:47471000-47472400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:47471000-47472600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr12:47471000-47472600	Transcr. at gene 5' and 3'	NH-A	brain
47	chr12:47471000-47472800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
48	chr12:47471000-47472800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin

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