Variant report

Variant	rs1473840
Chromosome Location	chr1:46601197-46601198
allele	C/T
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	SMC3	chr1:46600520-46601498	Hela-S3	cervix:	n/a	n/a
2	EP300	chr1:46600280-46601697	ECC-1	luminal epithelium:	n/a	n/a
3	NFIC	chr1:46600466-46601667	ECC-1	luminal epithelium:	n/a	n/a
4	MYC	chr1:46600419-46601571	MCF10A-Er-Src	breast:	n/a	n/a
5	JUND	chr1:46600353-46601460	Hela-S3	cervix:	n/a	chr1:46600577-46600588
6	STAT3	chr1:46600473-46601339	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
7	TFAP2C	chr1:46600412-46601492	Hela-S3	cervix:	n/a	chr1:46600834-46600849
8	RAD21	chr1:46600496-46601496	Hela-S3	cervix:	n/a	n/a
9	MXI1	chr1:46600431-46601538	Hela-S3	cervix:	n/a	n/a
10	FOS	chr1:46600426-46601534	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
11	STAT3	chr1:46600434-46601345	Hela-S3	cervix:	n/a	chr1:46600473-46600484
12	TBP	chr1:46600467-46601575	Hela-S3	cervix:	n/a	n/a
13	JUN	chr1:46600496-46601452	Hela-S3	cervix:	n/a	chr1:46600577-46600588
14	FOS	chr1:46600359-46601571	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
15	FOS	chr1:46601155-46601479	MCF10A-Er-Src	breast:	n/a	n/a
16	BRCA1	chr1:46600296-46601246	Hela-S3	cervix:	n/a	n/a
17	SMARCC1	chr1:46600405-46601507	Hela-S3	cervix:	n/a	n/a
18	SIN3AK20	chr1:46600379-46601254	MCF-7	breast:	n/a	n/a
19	CEBPB	chr1:46600382-46601605	Hela-S3	cervix:	n/a	chr1:46600679-46600690
20	FOS	chr1:46600359-46601501	MCF10A-Er-Src	breast:	n/a	chr1:46600577-46600588
21	GTF2F1	chr1:46600263-46601436	Hela-S3	cervix:	n/a	n/a
22	GTF3C2	chr1:46601153-46601738	Hela-S3	cervix:	n/a	n/a
23	NFIC	chr1:46600982-46601533	SK-N-SH	brain:	n/a	n/a
24	EP300	chr1:46600419-46601464	Hela-S3	cervix:	n/a	n/a
25	STAT3	chr1:46600378-46601500	MCF10A-Er-Src	breast:	n/a	chr1:46600473-46600484
26	RFX5	chr1:46600468-46601493	Hela-S3	cervix:	n/a	n/a
27	NFIC	chr1:46600533-46601658	ECC-1	luminal epithelium:	n/a	n/a
28	MYC	chr1:46600419-46601597	MCF10A-Er-Src	breast:	n/a	n/a
29	MAX	chr1:46600352-46601606	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
2	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
3	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
4	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
5	chr1:46598477..46601244-chr1:46712967..46714555,2	K562	blood:
6	chr1:46600538..46602719-chr1:109690592..109692888,2	MCF-7	breast:

Variant related genes	Relation type
PIK3R3	TF binding region
ENSG00000085999	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11211257	0.80[ASN][1000 genomes]
rs12090501	0.85[ASN][1000 genomes]
rs1416706	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707302	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1707303	0.89[ASN][1000 genomes]
rs4660341	0.84[ASN][1000 genomes]
rs785483	0.81[ASN][1000 genomes]
rs785484	0.84[ASN][1000 genomes]
rs785486	0.84[ASN][1000 genomes]
rs785490	0.84[ASN][1000 genomes]
rs785493	0.84[ASN][1000 genomes]
rs785496	0.84[ASN][1000 genomes]
rs785497	0.84[ASN][1000 genomes]
rs785499	0.81[ASN][1000 genomes]
rs785500	0.83[ASN][1000 genomes]
rs785504	0.89[ASN][1000 genomes]
rs785516	0.82[ASN][1000 genomes]
rs785517	0.84[ASN][1000 genomes]
rs785519	0.84[ASN][1000 genomes]
rs796773	0.83[ASN][1000 genomes]
rs9429095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473840	MAST2	cis	Artery Tibial	GTEx
rs1473840	IPP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599200-46601600	Flanking Active TSS	Hela-S3	cervix
2	chr1:46599200-46603200	Weak transcription	Ovary	ovary
3	chr1:46599400-46601200	Flanking Active TSS	Fetal Heart	heart
4	chr1:46599400-46602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:46599400-46603200	Weak transcription	Liver	Liver
6	chr1:46599600-46601200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:46599600-46601200	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr1:46599600-46601200	Enhancers	Fetal Stomach	stomach
9	chr1:46599600-46601400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:46599600-46601400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:46599600-46601600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr1:46599600-46601600	Enhancers	Fetal Muscle Leg	muscle
13	chr1:46599600-46601600	Enhancers	Left Ventricle	heart
14	chr1:46599600-46603200	Weak transcription	HSMMtube	muscle
15	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:46599800-46601200	Enhancers	HMEC	breast
17	chr1:46599800-46601600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr1:46599800-46603200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:46600000-46601400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:46600000-46601600	Enhancers	Fetal Brain Female	brain
21	chr1:46600000-46601800	Enhancers	Fetal Brain Male	brain
22	chr1:46600000-46602400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:46600000-46602400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:46600000-46602600	Weak transcription	Fetal Kidney	kidney
25	chr1:46600000-46603200	Weak transcription	HUVEC	blood vessel
26	chr1:46600000-46604000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:46600200-46601200	Enhancers	NHDF-Ad	bronchial
28	chr1:46600200-46601800	Enhancers	NHEK	skin
29	chr1:46600200-46603200	Weak transcription	Fetal Intestine Large	intestine
30	chr1:46600200-46603200	Weak transcription	Fetal Lung	lung
31	chr1:46600400-46601600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:46600400-46602200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:46600400-46602200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:46600400-46602400	Weak transcription	Aorta	Aorta
35	chr1:46600400-46602400	Weak transcription	Right Atrium	heart
36	chr1:46600600-46601200	Enhancers	Colon Smooth Muscle	Colon
37	chr1:46600600-46601200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr1:46600600-46601400	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:46600600-46601400	Enhancers	Osteobl	bone
40	chr1:46600600-46602200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:46600600-46603400	Weak transcription	HSMM	muscle
42	chr1:46600800-46601200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:46600800-46602400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:46600800-46602600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:46601000-46601200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:46601000-46601200	Enhancers	GM12878-XiMat	blood
47	chr1:46601000-46601400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:46601000-46601400	Weak transcription	Brain Germinal Matrix	brain
49	chr1:46601000-46602200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:46601000-46602200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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