Variant report

Variant	rs73831407
Chromosome Location	chr3:46968981-46968982
allele	A/G
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	PAX5	chr3:46968571-46969053	GM12891	blood:	n/a	chr3:46968830-46968839
2	PML	chr3:46968609-46969042	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:46967180-46969276	GM19099	blood:	n/a	n/a
4	POLR2A	chr3:46966327-46969602	GM12878	blood:	n/a	n/a
5	SP1	chr3:46968269-46969143	GM12878	blood:	n/a	n/a
6	FOXM1	chr3:46967934-46969255	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:46967958-46969376	K562	blood:	n/a	n/a
8	EBF1	chr3:46968063-46969292	GM12878	blood:	n/a	chr3:46968194-46968203 chr3:46968900-46968911
9	RXRA	chr3:46968545-46969007	GM12878	blood:	n/a	chr3:46968830-46968839
10	RUNX3	chr3:46968037-46969500	GM12878	blood:	n/a	n/a
11	YY1	chr3:46968239-46969427	GM12878	blood:	n/a	chr3:46968603-46968614
12	POLR2A	chr3:46966735-46970133	GM12878	blood:	n/a	n/a
13	RUNX3	chr3:46967320-46969539	GM12878	blood:	n/a	n/a
14	SPI1	chr3:46968131-46969179	GM12891	blood:	n/a	chr3:46968823-46968836 chr3:46968166-46968179
15	STAT1	chr3:46968288-46969150	GM12878	blood:	n/a	chr3:46968830-46968841 chr3:46968696-46968708 chr3:46968403-46968410 chr3:46968321-46968329
16	NFATC1	chr3:46968204-46969145	GM12878	blood:	n/a	n/a
17	ELF1	chr3:46968160-46969095	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:46967468-46969287	GM12892	blood:	n/a	n/a
19	IRF4	chr3:46968315-46969260	GM12878	blood:	n/a	n/a
20	ATF2	chr3:46968000-46969217	GM12878	blood:	n/a	n/a
21	STAT3	chr3:46968350-46969047	GM12878	blood:	n/a	chr3:46968830-46968841 chr3:46968696-46968708 chr3:46968403-46968410
22	MEF2A	chr3:46968241-46969211	GM12878	blood:	n/a	n/a
23	STAT5A	chr3:46968240-46969129	GM12878	blood:	n/a	chr3:46968254-46968266 chr3:46968830-46968841 chr3:46968696-46968708 chr3:46968403-46968410 chr3:46968321-46968329
24	MAX	chr3:46968231-46969144	GM12878	blood:	n/a	n/a
25	YY1	chr3:46968265-46969088	GM12892	blood:	n/a	chr3:46968603-46968614
26	SMC3	chr3:46968227-46969148	GM12878	blood:	n/a	n/a
27	PAX5	chr3:46968247-46969346	GM12878	blood:	n/a	chr3:46968830-46968839
28	POU2F2	chr3:46968203-46969627	GM12891	blood:	n/a	n/a
29	CHD1	chr3:46968119-46969339	GM12878	blood:	n/a	chr3:46969055-46969065
30	SPI1	chr3:46968085-46969541	GM12878	blood:	n/a	chr3:46969350-46969363 chr3:46968823-46968836 chr3:46968166-46968179
31	REST	chr3:46968706-46969009	Hela-S3	cervix:	n/a	n/a
32	BHLHE40	chr3:46968344-46969227	GM12878	blood:	n/a	n/a
33	RCOR1	chr3:46968340-46969198	GM12878	blood:	n/a	n/a
34	RELA	chr3:46968183-46969265	GM19099	blood:	n/a	n/a
35	MXI1	chr3:46968409-46969183	GM12878	blood:	n/a	n/a
36	TCF12	chr3:46968078-46969129	GM12878	blood:	n/a	chr3:46968141-46968151 chr3:46968275-46968282 chr3:46968117-46968127
37	MTA3	chr3:46966876-46970269	GM12878	blood:	n/a	n/a
38	BATF	chr3:46968434-46969163	GM12878	blood:	n/a	n/a
39	MEF2C	chr3:46968212-46969234	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:46966700-46969363	GM18951	blood:	n/a	n/a
41	SPI1	chr3:46968184-46969165	HL-60	blood:	n/a	chr3:46968823-46968836
42	CEBPB	chr3:46968700-46969020	GM12878	blood:	n/a	n/a
43	MTA3	chr3:46968092-46969485	GM12878	blood:	n/a	n/a
44	IRF4	chr3:46968242-46969204	GM12878	blood:	n/a	n/a
45	RELA	chr3:46968273-46969189	GM18505	blood:	n/a	n/a
46	POLR2A	chr3:46967011-46969467	GM12891	blood:	n/a	n/a
47	ELF1	chr3:46967998-46969492	GM12878	blood:	n/a	n/a
48	BCLAF1	chr3:46968264-46969431	GM12878	blood:	n/a	chr3:46968830-46968839
49	ZNF143	chr3:46968326-46969188	GM12878	blood:	n/a	chr3:46968671-46968690 chr3:46968948-46968957 chr3:46968667-46968685
50	NFIC	chr3:46968093-46970282	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:46968433..46974874-chr3:46985986..46991697,10	MCF-7	breast:
2	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
3	chr3:46964830..46966605-chr3:46968655..46970497,2	K562	blood:
4	chr3:46967003..46969518-chr3:47029296..47031281,2	K562	blood:
5	chr3:46967003..46969094-chr3:47027907..47030796,2	K562	blood:
6	chr3:46968346..46971125-chr3:47016848..47020508,3	K562	blood:
7	chr3:46968594..46970505-chr3:47016848..47019482,2	K562	blood:
8	chr3:46965883..46969429-chr3:47022291..47025425,4	MCF-7	breast:
9	chr3:46966646..46969252-chr3:47031389..47034280,2	MCF-7	breast:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs17079248	1.00[AMR][1000 genomes]
rs55633581	1.00[AFR][1000 genomes]
rs55727789	0.83[AFR][1000 genomes]
rs55730344	0.83[AFR][1000 genomes]
rs55832326	0.83[AFR][1000 genomes]
rs56329054	1.00[AFR][1000 genomes]
rs57341796	1.00[AFR][1000 genomes]
rs58529346	1.00[AFR][1000 genomes]
rs59608805	1.00[AMR][1000 genomes]
rs60100816	0.83[AFR][1000 genomes]
rs72895218	1.00[AMR][1000 genomes]
rs73831404	1.00[AMR][1000 genomes]
rs73831412	0.83[AFR][1000 genomes]
rs73831415	1.00[AFR][1000 genomes]
rs73831421	1.00[AFR][1000 genomes]
rs73831424	0.83[AFR][1000 genomes]
rs73831425	0.83[AFR][1000 genomes]
rs73831428	0.83[AFR][1000 genomes]
rs73831430	0.83[AFR][1000 genomes]
rs73831431	0.83[AFR][1000 genomes]
rs73831432	0.83[AFR][1000 genomes]
rs73831444	0.83[AFR][1000 genomes]
rs73831445	0.83[AFR][1000 genomes]
rs73831446	0.83[AFR][1000 genomes]
rs73831448	0.83[AFR][1000 genomes]
rs73831449	0.83[AFR][1000 genomes]
rs73831450	1.00[AFR][1000 genomes]
rs73831451	0.83[AFR][1000 genomes]
rs73831453	0.83[AFR][1000 genomes]
rs73831455	0.83[AFR][1000 genomes]
rs73831457	0.83[AFR][1000 genomes]
rs73831458	0.83[AFR][1000 genomes]
rs73831459	0.83[AFR][1000 genomes]
rs73831466	0.83[AFR][1000 genomes]
rs73831467	0.83[AFR][1000 genomes]
rs73833639	1.00[AMR][1000 genomes]
rs73833643	1.00[AMR][1000 genomes]
rs73833661	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases
8	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46958600-46970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:46959000-46971400	Strong transcription	K562	blood
3	chr3:46959600-46970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:46959800-46969200	Strong transcription	NHEK	skin
5	chr3:46959800-46971200	Strong transcription	Hela-S3	cervix
6	chr3:46960200-46971200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr3:46960400-46969400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:46960400-46970400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:46960400-46970400	Strong transcription	Fetal Lung	lung
10	chr3:46960600-46969800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:46961000-46970000	Strong transcription	Brain Germinal Matrix	brain
12	chr3:46961400-46970400	Strong transcription	Fetal Brain Female	brain
13	chr3:46961800-46971200	Strong transcription	HepG2	liver
14	chr3:46962000-46969200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:46962600-46969200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:46962600-46972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:46962800-46972400	Weak transcription	Fetal Kidney	kidney
18	chr3:46964000-46970200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:46964200-46970000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:46964400-46969600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:46964600-46969400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:46964600-46969400	Genic enhancers	Stomach Smooth Muscle	stomach
23	chr3:46964600-46975600	Weak transcription	Fetal Brain Male	brain
24	chr3:46964800-46969400	Genic enhancers	Gastric	stomach
25	chr3:46964800-46972800	Enhancers	Fetal Heart	heart
26	chr3:46965000-46969600	Genic enhancers	Right Ventricle	heart
27	chr3:46965000-46971200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:46965400-46969600	Genic enhancers	Fetal Muscle Trunk	muscle
29	chr3:46965400-46970000	Genic enhancers	Esophagus	oesophagus
30	chr3:46965800-46969800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:46965800-46970000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:46966000-46969800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:46966400-46969600	Enhancers	Right Atrium	heart
34	chr3:46966400-46969800	Genic enhancers	Fetal Muscle Leg	muscle
35	chr3:46966400-46971400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:46966600-46970000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:46966600-46970000	Genic enhancers	Fetal Thymus	thymus
38	chr3:46966800-46969600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:46966800-46969600	Genic enhancers	Lung	lung
40	chr3:46967000-46970800	Weak transcription	Aorta	Aorta
41	chr3:46967000-46972400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:46967200-46969200	Genic enhancers	Thymus	Thymus
43	chr3:46967200-46969400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr3:46967200-46969400	Genic enhancers	A549	lung
45	chr3:46967200-46969400	Genic enhancers	HSMM	muscle
46	chr3:46967200-46970200	Enhancers	Psoas Muscle	Psoas
47	chr3:46967200-46970800	Weak transcription	HMEC	breast
48	chr3:46967200-46971200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:46967200-46971800	Weak transcription	Ovary	ovary
50	chr3:46967400-46969400	Flanking Active TSS	Primary B cells from cord blood	blood

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