Variant report

Variant	rs789721
Chromosome Location	chr12:64588565-64588566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64586725..64590184-chr12:64613971..64617345,3	MCF-7	breast:
2	chr12:64234749..64237107-chr12:64586923..64589437,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243024	Chromatin interaction
ENSG00000174206	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10748003	0.83[AMR][1000 genomes]
rs1086318	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1086319	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10878118	0.82[AMR][1000 genomes]
rs10878126	0.82[LWK][hapmap];0.88[MKK][hapmap];0.96[YRI][hapmap]
rs1162975	0.86[YRI][hapmap]
rs1464055	0.96[YRI][hapmap]
rs1695105	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865800	0.87[CHB][hapmap]
rs2279740	0.87[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2643665	0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes]
rs34360383	0.90[ASN][1000 genomes]
rs699633	0.85[YRI][hapmap]
rs722526	0.80[TSI][hapmap]
rs789711	1.00[ASW][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs789712	0.84[AMR][1000 genomes]
rs789713	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs789749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs789750	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790011	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs790012	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9788007	0.80[AMR][1000 genomes]
rs9804707	0.81[CHB][hapmap]

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	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv3509287	chr12:64526217-64736995	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3509288	chr12:64526217-64736995	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64574600-64597000	Weak transcription	Esophagus	oesophagus
2	chr12:64575000-64615200	Weak transcription	Psoas Muscle	Psoas
3	chr12:64575200-64597000	Weak transcription	Aorta	Aorta
4	chr12:64575400-64590400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:64575600-64607600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:64575600-64615000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:64575800-64615200	Weak transcription	Fetal Stomach	stomach
8	chr12:64576000-64597200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:64576000-64615000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:64576200-64589600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:64581200-64597000	Weak transcription	HSMMtube	muscle
12	chr12:64581400-64614600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr12:64581600-64589000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:64581800-64588600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:64581800-64615400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:64582400-64588800	Weak transcription	NHLF	lung
17	chr12:64582600-64614600	Weak transcription	Hela-S3	cervix
18	chr12:64582600-64614600	Weak transcription	NHDF-Ad	bronchial
19	chr12:64583200-64589400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:64583200-64615400	Weak transcription	Placenta	Placenta
21	chr12:64584800-64615200	Weak transcription	Thymus	Thymus
22	chr12:64585400-64589000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:64585400-64589000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:64585800-64589000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:64586000-64611800	Weak transcription	Small Intestine	intestine
26	chr12:64586200-64589000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:64586200-64589000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:64586200-64589200	Strong transcription	Primary B cells from cord blood	blood
29	chr12:64586200-64589200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr12:64586200-64597800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:64586200-64615200	Weak transcription	Right Ventricle	heart
32	chr12:64586400-64589000	Strong transcription	Primary T cells from cord blood	blood
33	chr12:64586400-64599800	Weak transcription	Stomach Mucosa	stomach
34	chr12:64586600-64588600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:64586600-64589000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:64586800-64588600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:64586800-64589000	Strong transcription	Adipose Nuclei	Adipose
38	chr12:64586800-64589200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:64586800-64589200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:64586800-64589200	Strong transcription	Liver	Liver
41	chr12:64586800-64589400	Weak transcription	Colonic Mucosa	Colon
42	chr12:64586800-64604200	Weak transcription	Ovary	ovary
43	chr12:64587000-64589200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:64587200-64589000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:64587200-64589200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:64587400-64588600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:64587400-64588600	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr12:64587400-64589000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:64587400-64589000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr12:64587400-64589000	Strong transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links