Variant report

Variant	rs5001573
Chromosome Location	chr3:23991717-23991718
allele	C/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	TBP	chr3:23991592-23992064	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:23990907-23992320	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
4	IRF1	chr3:23991394-23992096	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
5	MEF2A	chr3:23991193-23991843	GM12878	blood:	n/a	chr3:23991524-23991545 chr3:23991526-23991541 chr3:23991528-23991539 chr3:23991524-23991545 chr3:23991526-23991540
6	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
7	ATF2	chr3:23991195-23992030	GM12878	blood:	n/a	n/a
8	IKZF1	chr3:23991262-23992018	GM12878	blood:	n/a	n/a
9	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
10	FOXA2	chr3:23990924-23991860	HepG2	liver:	n/a	n/a
11	RELA	chr3:23991372-23992198	GM19099	blood:	n/a	n/a
12	NFIC	chr3:23991143-23991883	GM12878	blood:	n/a	n/a
13	RUNX3	chr3:23991138-23991978	GM12878	blood:	n/a	n/a
14	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
15	MEF2A	chr3:23991241-23991850	GM12878	blood:	n/a	chr3:23991524-23991545 chr3:23991526-23991541 chr3:23991528-23991539 chr3:23991524-23991545 chr3:23991526-23991540
16	NFIC	chr3:23991233-23991798	GM12878	blood:	n/a	n/a
17	STAT1	chr3:23990981-23991915	GM12878	blood:	n/a	n/a
18	CTCF	chr3:23991644-23991844	GM12878	blood:	n/a	n/a
19	EBF1	chr3:23991058-23991743	GM12878	blood:	n/a	n/a
20	FOXM1	chr3:23991167-23991798	GM12878	blood:	n/a	n/a
21	CTCF	chr3:23991680-23991830	AG09319	gingival:	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
NKIRAS1	TF binding region
NR1D2	TF binding region
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1135452	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2001209	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4619736	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773828	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778970	0.88[ASN][1000 genomes]
rs6800407	0.88[ASN][1000 genomes]
rs72627066	0.88[ASN][1000 genomes]
rs7633520	0.95[ASN][1000 genomes]
rs9755750	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9862416	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5001573	NR1D2	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:23988400-23991800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
15	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
16	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:23989000-23992000	Enhancers	NHEK	skin
18	chr3:23989000-23992200	Enhancers	HepG2	liver
19	chr3:23989000-23992200	Enhancers	HMEC	breast
20	chr3:23989000-23993800	Enhancers	Liver	Liver
21	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:23989200-23992200	Enhancers	A549	lung
25	chr3:23989200-23992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
28	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
32	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
33	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:23989400-23992200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:23989400-23992200	Enhancers	Ovary	ovary
38	chr3:23989400-23992800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:23989400-23993800	Enhancers	Brain Anterior Caudate	brain
40	chr3:23989400-23994400	Enhancers	Brain Angular Gyrus	brain
41	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
43	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
45	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
46	chr3:23989800-23993200	Weak transcription	Brain Germinal Matrix	brain
47	chr3:23989800-23993400	Weak transcription	Gastric	stomach
48	chr3:23989800-23994600	Weak transcription	Lung	lung
49	chr3:23989800-23995600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:23989800-23996000	Weak transcription	Osteobl	bone

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