Variant report

Variant	rs58943141
Chromosome Location	chr12:104302739-104302740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:104302578-104303047	T-47D	breast:	n/a	n/a
2	TEAD4	chr12:104302673-104303090	ECC-1	luminal epithelium:	n/a	n/a
3	FOXA1	chr12:104302518-104302998	T-47D	breast:	n/a	n/a
4	TCF12	chr12:104302501-104303170	SK-N-SH	brain:	n/a	n/a
5	FOXA1	chr12:104302520-104303011	T-47D	breast:	n/a	n/a
6	POLR2A	chr12:104302654-104303030	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104300678..104303599-chr12:104319392..104323559,4	K562	blood:
2	chr12:104300942..104303237-chr12:104305354..104306983,2	K562	blood:
3	chr12:104296301..104298365-chr12:104301480..104303104,2	K562	blood:
4	chr12:104302164..104305303-chr12:104321451..104326533,4	MCF-7	breast:
5	chr12:104299931..104303136-chr12:104307150..104309681,4	K562	blood:
6	chr12:104301059..104305002-chr12:104308299..104311769,5	K562	blood:
7	chr12:104298858..104303101-chr12:104321689..104325332,4	K562	blood:
8	chr12:104301536..104303979-chr12:104529834..104532594,2	K562	blood:
9	chr12:104296301..104297835-chr12:104301480..104303235,2	K562	blood:
10	chr12:104300652..104303185-chr12:104457889..104460360,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000214198	TF binding region
ENSG00000166598	Chromatin interaction
ENSG00000214198	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000111727	Chromatin interaction
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10861144	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861145	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111825	0.81[ASN][1000 genomes]
rs11111829	0.81[ASN][1000 genomes]
rs11111833	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111835	1.00[ASN][1000 genomes]
rs11111837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11111842	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111849	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11111850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11830285	0.81[ASN][1000 genomes]
rs11831836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833702	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034931	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583273	0.93[ASN][1000 genomes]
rs3794246	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57083451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58929830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315947	0.81[ASN][1000 genomes]
rs73177915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177916	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73177918	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177919	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73177921	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104295800-104303000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr12:104295800-104303200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr12:104295800-104303800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr12:104299400-104303000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:104299800-104303000	Enhancers	Fetal Thymus	thymus
6	chr12:104301000-104303600	Weak transcription	Spleen	Spleen
7	chr12:104301400-104302800	Enhancers	Primary T cells fromperipheralblood	blood
8	chr12:104301400-104304200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:104301400-104304200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:104301400-104304200	Enhancers	HMEC	breast
11	chr12:104301400-104304400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr12:104301400-104304400	Enhancers	HSMMtube	muscle
13	chr12:104301800-104302800	Enhancers	GM12878-XiMat	blood
14	chr12:104302000-104303600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:104302200-104302800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:104302200-104303000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:104302200-104303000	Enhancers	Fetal Heart	heart
18	chr12:104302200-104303000	Enhancers	Placenta	Placenta
19	chr12:104302200-104303800	Enhancers	NHDF-Ad	bronchial
20	chr12:104302200-104304200	Enhancers	HSMM	muscle
21	chr12:104302200-104304200	Enhancers	Osteobl	bone
22	chr12:104302200-104304400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:104302400-104302800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:104302400-104302800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:104302400-104302800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:104302400-104303000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:104302400-104303200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:104302400-104304000	Weak transcription	Thymus	Thymus
29	chr12:104302400-104304200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:104302400-104304200	Enhancers	NHEK	skin
31	chr12:104302600-104302800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:104302600-104302800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr12:104302600-104302800	Enhancers	Gastric	stomach
34	chr12:104302600-104303000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr12:104302600-104303000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr12:104302600-104303000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr12:104302600-104303000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:104302600-104303000	Enhancers	NHLF	lung
39	chr12:104302600-104303600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:104302600-104304000	Enhancers	NH-A	brain

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