Variant report

Variant	rs7309973
Chromosome Location	chr12:104714224-104714225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104712593..104714934-chr12:104720568..104722674,2	MCF-7	breast:
2	chr12:104692670..104694537-chr12:104713011..104714682,2	K562	blood:
3	chr12:104714067..104716870-chr12:104718571..104721290,2	K562	blood:
4	chr12:104710591..104713638-chr12:104713688..104716815,3	K562	blood:
5	chr12:104696229..104700878-chr12:104707371..104714338,7	K562	blood:

Variant related genes	Relation type
ENSG00000255150	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10778323	0.82[YRI][hapmap];0.94[AFR][1000 genomes]
rs11111970	0.94[ASN][1000 genomes]
rs11111973	0.94[ASN][1000 genomes]
rs12318033	0.94[ASN][1000 genomes]
rs12368657	0.94[ASN][1000 genomes]
rs17035372	0.82[YRI][hapmap]
rs34195880	0.85[EUR][1000 genomes]
rs34407590	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34518697	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34612644	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35009941	1.00[ASN][1000 genomes]
rs35456434	1.00[ASN][1000 genomes]
rs35472124	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35764486	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4477504	0.96[AFR][1000 genomes]
rs4576900	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964753	0.94[ASN][1000 genomes]
rs4964781	0.93[AFR][1000 genomes]
rs58078551	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58716236	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539138	0.83[YRI][hapmap];0.97[AFR][1000 genomes]
rs7303284	0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7958103	0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS 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	32 gene(s)	inside rSNPs	diseases
3	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1048075	chr12:104694799-104751460	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv541588	chr12:104694799-104751460	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104683800-104723800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:104698000-104716200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:104698400-104716600	Strong transcription	HSMM	muscle
4	chr12:104698400-104718400	Weak transcription	Stomach Mucosa	stomach
5	chr12:104698400-104720600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:104698400-104747600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:104698600-104716200	Strong transcription	NHEK	skin
8	chr12:104699400-104728400	Weak transcription	Fetal Heart	heart
9	chr12:104701000-104724400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:104701600-104733600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:104702000-104716200	Strong transcription	NH-A	brain
12	chr12:104702000-104733600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:104702400-104715600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:104702400-104746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:104702400-104747400	Strong transcription	Dnd41	blood
16	chr12:104702600-104716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:104703000-104716400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:104703000-104716600	Strong transcription	Fetal Thymus	thymus
19	chr12:104703000-104716800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:104703000-104722400	Strong transcription	K562	blood
21	chr12:104703000-104749200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:104703400-104716800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:104703400-104738400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:104703400-104747800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:104703600-104724200	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:104703600-104744000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:104703800-104716000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:104703800-104733000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:104704400-104743600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:104704600-104715800	Strong transcription	Left Ventricle	heart
31	chr12:104704600-104716000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:104704600-104716600	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:104704600-104716600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:104704600-104716800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:104704600-104724200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:104704800-104715000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:104704800-104715800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:104704800-104716400	Strong transcription	Primary T cells from cord blood	blood
39	chr12:104704800-104716400	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:104704800-104726400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:104704800-104747200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:104705000-104715200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:104705000-104716200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr12:104705000-104716200	Strong transcription	HepG2	liver
45	chr12:104705000-104716400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:104705000-104716600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr12:104705000-104716600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr12:104705000-104716600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:104705000-104716600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:104705000-104716600	Strong transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links