Variant report

Variant	rs73177942
Chromosome Location	chr12:104355817-104355818
allele	A/G
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	POLR2A	chr12:104355788-104355979	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:104355797-104356802	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:104355599-104355898	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:104355170-104355987	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr12:104355625-104356841	K562	blood:	n/a	n/a
6	POLR2A	chr12:104355151-104355891	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:104355539-104355890	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104354928..104356634-chr12:104388334..104391099,2	MCF-7	breast:

Variant related genes	Relation type
C12orf73	TF binding region
TDG	TF binding region
ENSG00000120820	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17034968	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034974	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249210	0.98[ASN][1000 genomes]
rs2293621	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583259	0.98[ASN][1000 genomes]
rs2722193	1.00[ASN][1000 genomes]
rs2722195	1.00[ASN][1000 genomes]
rs3763995	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763996	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135042	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135067	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4135077	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964142	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964163	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964164	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73177938	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177950	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs812498	1.00[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	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104351400-104358000	Weak transcription	Lung	lung
2	chr12:104351400-104358000	Weak transcription	Spleen	Spleen
3	chr12:104351600-104356200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:104351600-104356400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:104351600-104356400	Weak transcription	Brain Angular Gyrus	brain
6	chr12:104351600-104357000	Weak transcription	Fetal Brain Female	brain
7	chr12:104351600-104357200	Weak transcription	GM12878-XiMat	blood
8	chr12:104351600-104357400	Weak transcription	Fetal Lung	lung
9	chr12:104351600-104357400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:104351600-104357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr12:104351600-104357600	Weak transcription	NHLF	lung
12	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
17	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
18	chr12:104351600-104357800	Weak transcription	NHEK	skin
19	chr12:104351600-104357800	Weak transcription	Osteobl	bone
20	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
26	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
27	chr12:104351600-104358000	Weak transcription	Ovary	ovary
28	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
30	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
31	chr12:104351600-104358000	Weak transcription	HMEC	breast
32	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
39	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
40	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
41	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
42	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:104352000-104356200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:104352000-104357600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:104352000-104357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:104352000-104357800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:104352000-104357800	Weak transcription	Adipose Nuclei	Adipose
50	chr12:104352000-104357800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links