Variant report

Variant	rs56219801
Chromosome Location	chr12:104356429-104356430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:104356397-104356685	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:104356346-104356793	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:104356338-104356762	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:104355797-104356802	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr12:104356234-104357190	HepG2	liver:	n/a	n/a
6	POU2F2	chr12:104356307-104356663	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:104356173-104356867	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:104356420-104356686	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:104356154-104356747	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr12:104356287-104356803	GM12892	blood:	n/a	n/a
11	POU2F2	chr12:104356258-104356711	GM12891	blood:	n/a	n/a
12	POLR2A	chr12:104356331-104356769	GM12892	blood:	n/a	n/a
13	TBP	chr12:104356363-104356687	GM12878	blood:	n/a	n/a
14	HEY1	chr12:104356417-104356697	K562	blood:	n/a	n/a
15	POLR2A	chr12:104356251-104356675	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:104356397-104356580	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:104356217-104356796	MCF-7	breast:	n/a	n/a
18	POLR2A	chr12:104356133-104356729	K562	blood:	n/a	n/a
19	POLR2A	chr12:104356322-104356802	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:104356330-104356729	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr12:104356272-104356854	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:104356140-104357240	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr12:104356239-104356757	Raji	blood:	n/a	n/a
24	POLR2A	chr12:104356316-104356854	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:104355625-104356841	K562	blood:	n/a	n/a
26	POLR2A	chr12:104356408-104356685	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr12:104356424-104356468	ProgFib	skin:	n/a	n/a
28	POLR2A	chr12:104356234-104356662	GM12878	blood:	n/a	n/a
29	TBP	chr12:104356377-104356705	K562	blood:	n/a	n/a
30	POLR2A	chr12:104356266-104356797	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:104356258-104356797	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:104356267-104357115	K562	blood:	n/a	n/a
33	POLR2A	chr12:104356247-104356722	HepG2	liver:	n/a	n/a
34	POLR2A	chr12:104356136-104356653	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr12:104356199-104356712	K562	blood:	n/a	n/a
36	POLR2A	chr12:104356231-104356735	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr12:104356361-104356712	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr12:104356427-104356691	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
2	chr12:104354928..104356634-chr12:104388334..104391099,2	MCF-7	breast:
3	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
4	chr12:104324052..104326463-chr12:104355875..104358112,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDG-1	chr12:104356173-104356953	NONHSAT030400

No data

Variant related genes	Relation type
TDG	TF binding region
ENSG00000265072	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10047614	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861150	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861151	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366629	1.00[ASN][1000 genomes]
rs12369231	1.00[ASN][1000 genomes]
rs12372540	1.00[ASN][1000 genomes]
rs17805003	1.00[ASN][1000 genomes]
rs1866074	1.00[ASN][1000 genomes]
rs4135044	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135063	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135081	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4135093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55684344	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369424	1.00[ASN][1000 genomes]
rs6539116	1.00[ASN][1000 genomes]
rs7136550	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138850	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306515	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313381	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];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	chr12:104351600-104357000	Weak transcription	Fetal Brain Female	brain
4	chr12:104351600-104357200	Weak transcription	GM12878-XiMat	blood
5	chr12:104351600-104357400	Weak transcription	Fetal Lung	lung
6	chr12:104351600-104357400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:104351600-104357600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:104351600-104357600	Weak transcription	NHLF	lung
9	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
14	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
15	chr12:104351600-104357800	Weak transcription	NHEK	skin
16	chr12:104351600-104357800	Weak transcription	Osteobl	bone
17	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
23	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
24	chr12:104351600-104358000	Weak transcription	Ovary	ovary
25	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
27	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
28	chr12:104351600-104358000	Weak transcription	HMEC	breast
29	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
36	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
37	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
39	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:104352000-104357600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:104352000-104357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:104352000-104357800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:104352000-104357800	Weak transcription	Adipose Nuclei	Adipose
46	chr12:104352000-104357800	Weak transcription	Fetal Muscle Leg	muscle
47	chr12:104352000-104358000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr12:104352000-104358000	Weak transcription	Left Ventricle	heart
49	chr12:104352000-104358400	Weak transcription	Primary B cells from cord blood	blood
50	chr12:104352200-104357200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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