Variant report

Variant	rs6580783
Chromosome Location	chr12:51443724-51443725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51421719..51422616-chr12:51442889..51443788,2	MCF-7	breast:
2	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
3	chr12:51440588..51444188-chr12:51475693..51478745,10	K562	blood:
4	chr12:51440271..51447226-chr12:51475135..51479930,16	MCF-7	breast:
5	chr12:51418602..51423346-chr12:51439309..51444851,15	MCF-7	breast:
6	chr12:51439067..51445190-chr12:51449547..51456560,11	K562	blood:
7	chr12:51421116..51422954-chr12:51442627..51444321,2	K562	blood:
8	chr12:51157036..51159803-chr12:51442013..51443781,2	K562	blood:
9	chr12:51156477..51159239-chr12:51440349..51444629,5	K562	blood:
10	chr12:51440743..51444863-chr12:51448295..51453075,7	MCF-7	breast:
11	chr12:51440639..51443821-chr12:51630707..51634068,3	K562	blood:
12	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
13	chr12:51441811..51444855-chr12:51447426..51450145,3	K562	blood:
14	chr12:51440782..51445752-chr12:51631445..51635429,5	MCF-7	breast:
15	chr12:51441619..51444815-chr12:51631402..51636504,5	K562	blood:
16	chr12:51440588..51444188-chr12:51475774..51478819,7	K562	blood:
17	chr12:51440852..51445521-chr12:51475730..51478507,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000050426	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1026994	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783411	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783412	1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876126	1.00[ASN][1000 genomes]
rs11169679	1.00[ASN][1000 genomes]
rs11169718	1.00[JPT][hapmap]
rs11169724	1.00[JPT][hapmap]
rs12369066	1.00[JPT][hapmap]
rs12423207	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs150909	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs161044	0.89[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs161045	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs161046	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs161047	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17125367	1.00[JPT][hapmap]
rs17125370	1.00[JPT][hapmap]
rs17125416	1.00[JPT][hapmap]
rs17125418	1.00[JPT][hapmap]
rs17125428	1.00[JPT][hapmap]
rs17229232	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2029147	1.00[ASN][1000 genomes]
rs224564	1.00[ASN][1000 genomes]
rs224566	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs224569	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs224570	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs224573	0.89[ASW][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs224574	1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs224576	0.83[ASN][1000 genomes]
rs224578	1.00[ASN][1000 genomes]
rs224586	0.83[ASN][1000 genomes]
rs224590	0.82[AFR][1000 genomes]
rs224592	1.00[ASN][1000 genomes]
rs224593	1.00[ASN][1000 genomes]
rs2630362	0.89[ASW][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[ASN][1000 genomes]
rs364627	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs390424	0.80[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs394384	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs416062	1.00[ASN][1000 genomes]
rs4238110	1.00[ASN][1000 genomes]
rs435965	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs445520	1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs452587	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4768875	0.83[AFR][1000 genomes]
rs4768959	1.00[ASW][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768973	1.00[JPT][hapmap]
rs58309379	1.00[ASN][1000 genomes]
rs613977	1.00[ASN][1000 genomes]
rs6580779	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580780	1.00[ASN][1000 genomes]
rs686528	1.00[ASN][1000 genomes]
rs7299484	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7960097	1.00[JPT][hapmap]
rs7969536	1.00[ASN][1000 genomes]
rs7971712	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7972608	1.00[ASW][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7973541	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7974923	0.89[ASW][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975628	0.89[ASW][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977993	1.00[ASN][1000 genomes]
rs7978782	0.88[YRI][hapmap]
rs9739943	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580783	SLC11A2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51442600-51443800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:51442600-51443800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:51442600-51443800	Flanking Active TSS	Hela-S3	cervix
4	chr12:51442600-51443800	Flanking Active TSS	HUVEC	blood vessel
5	chr12:51442600-51443800	Flanking Active TSS	NHEK	skin
6	chr12:51442800-51443800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:51442800-51444000	Flanking Active TSS	Dnd41	blood
8	chr12:51442800-51448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:51442800-51449000	Weak transcription	Aorta	Aorta
10	chr12:51442800-51449800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:51442800-51450000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:51442800-51452800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:51442800-51470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:51443000-51443800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:51443000-51443800	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr12:51443000-51444400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr12:51443000-51445400	Weak transcription	Left Ventricle	heart
18	chr12:51443000-51445600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:51443000-51447000	Weak transcription	Lung	lung
20	chr12:51443000-51448200	Weak transcription	Gastric	stomach
21	chr12:51443000-51453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:51443200-51443800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:51443200-51443800	Flanking Active TSS	HepG2	liver
24	chr12:51443200-51443800	Transcr. at gene 5' and 3'	K562	blood
25	chr12:51443200-51444000	Enhancers	Primary hematopoietic stem cells	blood
26	chr12:51443200-51444000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:51443200-51447200	Weak transcription	Ovary	ovary
28	chr12:51443200-51447600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:51443200-51449600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:51443400-51443800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:51443400-51443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr12:51443400-51443800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:51443400-51443800	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:51443400-51443800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:51443400-51443800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:51443400-51443800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr12:51443400-51443800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:51443400-51443800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:51443400-51443800	Enhancers	Colon Smooth Muscle	Colon
40	chr12:51443400-51443800	Enhancers	Fetal Brain Female	brain
41	chr12:51443400-51443800	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:51443400-51443800	Transcr. at gene 5' and 3'	A549	lung
43	chr12:51443400-51444000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:51443400-51444000	Enhancers	Liver	Liver
45	chr12:51443400-51444000	Flanking Active TSS	GM12878-XiMat	blood
46	chr12:51443400-51444200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:51443400-51444200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:51443400-51444200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:51443400-51444200	Weak transcription	Placenta	Placenta
50	chr12:51443400-51445600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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