Variant report

Variant	rs73036780
Chromosome Location	chr3:23991297-23991298
allele	A/C
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	FOXA1	chr3:23991176-23991634	HepG2	liver:	n/a	n/a
2	FOXA1	chr3:23991237-23991541	T-47D	breast:	n/a	n/a
3	FOXA1	chr3:23991100-23991668	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:23990941-23991555	HepG2	liver:	n/a	n/a
5	FOXA2	chr3:23991244-23991545	A549	lung:	n/a	n/a
6	FOXA2	chr3:23991268-23991608	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:23990907-23992320	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
9	MEF2A	chr3:23991193-23991843	GM12878	blood:	n/a	chr3:23991524-23991545 chr3:23991526-23991541 chr3:23991528-23991539 chr3:23991524-23991545 chr3:23991526-23991540
10	MXI1	chr3:23991239-23991598	HepG2	liver:	n/a	n/a
11	SMC3	chr3:23991258-23991568	HepG2	liver:	n/a	n/a
12	MEF2C	chr3:23991139-23991724	GM12878	blood:	n/a	chr3:23991189-23991204 chr3:23991524-23991545 chr3:23991188-23991203 chr3:23991188-23991204 chr3:23991188-23991203 chr3:23991526-23991541 chr3:23991188-23991205 chr3:23991528-23991539 chr3:23991524-23991545 chr3:23991189-23991205 chr3:23991526-23991540
13	ATF2	chr3:23991195-23992030	GM12878	blood:	n/a	n/a
14	IKZF1	chr3:23991262-23992018	GM12878	blood:	n/a	n/a
15	IRF1	chr3:23990953-23992138	K562	blood:	n/a	chr3:23991957-23991971 chr3:23991960-23991973 chr3:23991959-23991979 chr3:23991961-23991971 chr3:23991963-23991977 chr3:23991960-23991973 chr3:23991955-23991976 chr3:23991955-23991972 chr3:23991960-23991974 chr3:23991965-23991978 chr3:23991957-23991974 chr3:23991960-23991971 chr3:23992018-23992035 chr3:23991960-23991972 chr3:23991959-23991973 chr3:23991960-23991973 chr3:23991961-23991975 chr3:23991959-23991970
16	RUNX3	chr3:23991235-23991654	GM12878	blood:	n/a	n/a
17	FOXA2	chr3:23990924-23991860	HepG2	liver:	n/a	n/a
18	NFIC	chr3:23991143-23991883	GM12878	blood:	n/a	n/a
19	RUNX3	chr3:23991138-23991978	GM12878	blood:	n/a	n/a
20	FOXA1	chr3:23991158-23991625	HepG2	liver:	n/a	n/a
21	IRF1	chr3:23991011-23992343	K562	blood:	n/a	chr3:23991957-23991971 chr3:23991960-23991973 chr3:23991959-23991979 chr3:23991961-23991971 chr3:23991963-23991977 chr3:23991960-23991973 chr3:23991955-23991976 chr3:23991955-23991972 chr3:23991960-23991974 chr3:23991965-23991978 chr3:23991957-23991974 chr3:23991960-23991971 chr3:23992018-23992035 chr3:23991960-23991972 chr3:23991959-23991973 chr3:23991960-23991973 chr3:23991961-23991975 chr3:23991959-23991970
22	MEF2A	chr3:23991241-23991850	GM12878	blood:	n/a	chr3:23991524-23991545 chr3:23991526-23991541 chr3:23991528-23991539 chr3:23991524-23991545 chr3:23991526-23991540
23	NFIC	chr3:23991233-23991798	GM12878	blood:	n/a	n/a
24	STAT1	chr3:23990981-23991915	GM12878	blood:	n/a	n/a
25	EBF1	chr3:23991058-23991743	GM12878	blood:	n/a	n/a
26	FOXA1	chr3:23991158-23991605	HepG2	liver:	n/a	n/a
27	FOXM1	chr3:23991167-23991798	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:23991229-23991579	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23988335..23991846-chr3:24002543..24006084,3	K562	blood:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
NR1D2	TF binding region
NKIRAS1	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11917128	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510558	0.87[EUR][1000 genomes]
rs55824572	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58241520	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036778	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036786	1.00[EUR][1000 genomes]
rs73036791	0.97[EUR][1000 genomes]
rs73036794	0.97[EUR][1000 genomes]
rs73036802	0.97[EUR][1000 genomes]
rs73038519	0.97[EUR][1000 genomes]
rs73038548	0.91[EUR][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
2	chr3:23988200-23992200	Enhancers	Small Intestine	intestine
3	chr3:23988200-23992200	Enhancers	Stomach Mucosa	stomach
4	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
5	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
6	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:23988400-23991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr3:23988400-23991600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:23988400-23991800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
17	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
18	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:23989000-23991400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:23989000-23991400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:23989000-23991400	Weak transcription	Fetal Intestine Large	intestine
22	chr3:23989000-23991400	Weak transcription	Fetal Stomach	stomach
23	chr3:23989000-23991600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:23989000-23991600	Enhancers	NHDF-Ad	bronchial
25	chr3:23989000-23991600	Enhancers	NHLF	lung
26	chr3:23989000-23992000	Enhancers	NHEK	skin
27	chr3:23989000-23992200	Enhancers	HepG2	liver
28	chr3:23989000-23992200	Enhancers	HMEC	breast
29	chr3:23989000-23993800	Enhancers	Liver	Liver
30	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:23989200-23991400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:23989200-23991400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:23989200-23991400	Enhancers	Hela-S3	cervix
36	chr3:23989200-23991600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:23989200-23991600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:23989200-23992200	Enhancers	A549	lung
39	chr3:23989200-23992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
42	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
46	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
47	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:23989400-23991400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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