Variant report

Variant	rs3020779
Chromosome Location	chr3:49724808-49724809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr3:49723221-49724844	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:49724748-49725481	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:49721456-49727648	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:49723734-49725129	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49717503-49727239	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49720128-49724935	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:49724738-49724992	K562	blood:	n/a	n/a
8	POLR2A	chr3:49722602-49725401	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:49716580-49724829	HepG2	liver:	n/a	n/a
10	TCF3	chr3:49724721-49724972	GM12878	blood:	n/a	n/a
11	POU2F2	chr3:49723701-49724861	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:49724766-49724921	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49724519-49724923	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:49724356-49724843	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:49723739-49724949	H1-hESC	embryonic stem cell:	n/a	n/a
16	EBF1	chr3:49724732-49724981	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:49724591-49727617	MCF10A-Er-Src	breast:	n/a	n/a
18	HEY1	chr3:49718256-49727412	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:49722625-49725083	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOSL2	chr3:49723695-49727217	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49710552..49715225-chr3:49718907..49727364,14	MCF-7	breast:
2	chr3:49724349..49727675-chr3:49755739..49757510,3	MCF-7	breast:
3	chr1:17086818..17089262-chr3:49723617..49726310,2	MCF-7	breast:
4	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:
5	chr3:49724739..49727802-chr3:49735823..49739048,3	MCF-7	breast:
6	chr3:49711727..49717769-chr3:49722772..49726950,7	K562	blood:
7	chr1:16964923..16974624-chr3:49722461..49732046,16	K562	blood:
8	chr3:49709764..49714141-chr3:49724462..49728582,8	MCF-7	breast:
9	chr3:49720877..49722933-chr3:49723247..49725096,3	K562	blood:
10	chr3:49719726..49722448-chr3:49723596..49725872,2	K562	blood:
11	chr3:49448668..49451033-chr3:49723995..49726731,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNF123	TF binding region
MST1	TF binding region
ENSG00000259970	TF binding region
ENSG00000186715	Chromatin interaction
ENSG00000259970	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000186301	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173531	Chromatin interaction
ENSG00000145022	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000215908	Chromatin interaction
ENSG00000176020	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1078341	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865956	0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	0.93[CEU][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap];0.81[YRI][hapmap]
rs11130217	1.00[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709734	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.86[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs12715437	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096480	0.88[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13322887	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1463728	1.00[ASN][1000 genomes]
rs1491983	0.93[CEU][hapmap]
rs1491985	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532204	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799844	0.81[EUR][1000 genomes]
rs1982861	0.86[YRI][hapmap]
rs1996663	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs2029591	0.93[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs2131108	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140270	1.00[ASN][1000 genomes]
rs2177268	1.00[ASN][1000 genomes]
rs2312462	0.86[YRI][hapmap]
rs2329021	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535523	0.81[EUR][1000 genomes]
rs34890793	0.93[CEU][hapmap]
rs35129566	0.81[EUR][1000 genomes]
rs4241405	0.93[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs4241407	0.86[YRI][hapmap]
rs4855833	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4855845	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855846	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855848	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855849	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap]
rs4855885	1.00[CEU][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997059	0.81[EUR][1000 genomes]
rs56127630	1.00[ASN][1000 genomes]
rs58339610	0.81[EUR][1000 genomes]
rs59684465	0.81[EUR][1000 genomes]
rs61557789	0.81[EUR][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62259947	1.00[ASN][1000 genomes]
rs62260663	0.81[EUR][1000 genomes]
rs62260720	0.81[EUR][1000 genomes]
rs62260723	0.81[EUR][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs62262722	0.86[EUR][1000 genomes]
rs62262730	0.83[EUR][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446285	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs6446286	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap]
rs6785045	1.00[ASN][1000 genomes]
rs6790568	0.81[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs6804970	0.83[EUR][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs73088137	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7620848	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs7621797	0.82[EUR][1000 genomes]
rs7628207	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7637711	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs7638750	1.00[ASN][1000 genomes]
rs7644148	0.82[YRI][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7648995	1.00[ASN][1000 genomes]
rs7649428	0.81[EUR][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9817807	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs9830730	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835157	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs9836756	0.81[EUR][1000 genomes]
rs9849038	1.00[CEU][hapmap]
rs9851651	0.81[EUR][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9861027	1.00[ASN][1000 genomes]
rs9870755	1.00[CEU][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs9870858	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs9871024	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv11877	chr3:49721171-49727086	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv471425	chr3:49721381-49726196	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
9	nsv482080	chr3:49721381-49726196	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	nsv822077	chr3:49721400-49734526	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
11	esv1825475	chr3:49722732-49734243	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3020779	AMT	cis	lung	GTEx
rs3020779	AMT	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49712800-49726200	Weak transcription	Small Intestine	intestine
2	chr3:49719000-49726200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:49720600-49726200	Weak transcription	A549	lung
4	chr3:49721000-49726200	Weak transcription	HSMM	muscle
5	chr3:49721400-49725800	Weak transcription	Hela-S3	cervix
6	chr3:49721400-49725800	Weak transcription	K562	blood
7	chr3:49721400-49726400	Weak transcription	Aorta	Aorta
8	chr3:49721600-49726200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:49722400-49726200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:49723000-49725000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr3:49723200-49725000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:49723200-49725000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr3:49723200-49725000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr3:49723200-49725600	Weak transcription	Dnd41	blood
15	chr3:49723400-49725000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:49723400-49725000	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr3:49723400-49725000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:49723400-49725200	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:49723400-49725800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49723400-49725800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:49723400-49726400	Weak transcription	Lung	lung
22	chr3:49723800-49725000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:49723800-49725000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:49723800-49725000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:49723800-49725200	Active TSS	Gastric	stomach
26	chr3:49724200-49726200	Weak transcription	Ovary	ovary
27	chr3:49724200-49726200	Weak transcription	NHLF	lung
28	chr3:49724400-49725000	Enhancers	Fetal Heart	heart
29	chr3:49724400-49725000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr3:49724400-49725800	Weak transcription	GM12878-XiMat	blood
31	chr3:49724400-49726200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:49724400-49726200	Weak transcription	Psoas Muscle	Psoas
33	chr3:49724400-49726400	Enhancers	Spleen	Spleen
34	chr3:49724600-49725000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
35	chr3:49724600-49725000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:49724600-49725000	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr3:49724600-49725200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:49724600-49725200	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr3:49724600-49725200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr3:49724600-49725400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr3:49724600-49726000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:49724600-49726000	Weak transcription	Brain Angular Gyrus	brain
43	chr3:49724600-49726000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:49724600-49726200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:49724600-49726200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr3:49724600-49726200	Weak transcription	Fetal Kidney	kidney
47	chr3:49724600-49726200	Weak transcription	Left Ventricle	heart
48	chr3:49724600-49726400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr3:49724800-49725000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr3:49724800-49725000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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