Variant report

Variant	rs58241520
Chromosome Location	chr3:23989215-23989216
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	TCF7L2	chr3:23988923-23989506	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr3:23988647-23989955	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:23988782-23989327	SK-N-SH	brain:	n/a	n/a
4	EP300	chr3:23989126-23989434	GM12878	blood:	n/a	n/a
5	MYC	chr3:23988765-23989282	K562	blood:	n/a	n/a
6	NFIC	chr3:23988733-23989420	ECC-1	luminal epithelium:	n/a	n/a
7	MAFK	chr3:23988848-23989313	IMR90	lung:	n/a	n/a
8	MXI1	chr3:23988969-23989347	Hela-S3	cervix:	n/a	n/a
9	MYC	chr3:23988783-23989296	MCF10A-Er-Src	breast:	n/a	n/a
10	EP300	chr3:23988957-23989315	Hela-S3	cervix:	n/a	n/a
11	RCOR1	chr3:23988970-23989250	Hela-S3	cervix:	n/a	n/a
12	RXRA	chr3:23988783-23989298	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:23988850-23989284	U87	brain:	n/a	n/a
14	RFX5	chr3:23988280-23989331	K562	blood:	n/a	chr3:23988706-23988723
15	BACH1	chr3:23988883-23989248	H1-hESC	embryonic stem cell:	n/a	n/a
16	TAL1	chr3:23989076-23989846	K562	blood:	n/a	n/a
17	BHLHE40	chr3:23988803-23989327	K562	blood:	n/a	n/a
18	JUN	chr3:23988695-23989298	HUVEC	blood vessel:	n/a	n/a
19	ARID3A	chr3:23988644-23989296	K562	blood:	n/a	n/a
20	CEBPB	chr3:23988884-23989342	IMR90	lung:	n/a	n/a
21	STAT3	chr3:23988893-23989282	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr3:23988827-23989334	MCF10A-Er-Src	breast:	n/a	chr3:23989083-23989094
23	MAX	chr3:23988804-23989258	Hela-S3	cervix:	n/a	n/a
24	E2F4	chr3:23988933-23989220	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr3:23988780-23989316	HUVEC	blood vessel:	n/a	chr3:23989083-23989094
26	MAZ	chr3:23986016-23989986	IMR90	lung:	n/a	chr3:23988135-23988144 chr3:23986729-23986739 chr3:23987160-23987170 chr3:23987346-23987355 chr3:23987347-23987354 chr3:23987882-23987891 chr3:23987345-23987355 chr3:23987346-23987355 chr3:23987345-23987356
27	FOS	chr3:23988840-23989338	MCF10A-Er-Src	breast:	n/a	chr3:23989083-23989094
28	TCF12	chr3:23988687-23989530	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr3:23988852-23989306	HCT-116	colon:	n/a	n/a
30	POLR2A	chr3:23988855-23989284	U87	brain:	n/a	n/a
31	POLR2A	chr3:23988774-23992252	A549	lung:	n/a	n/a
32	POLR2A	chr3:23988626-23989318	H1-hESC	embryonic stem cell:	n/a	n/a
33	PBX3	chr3:23988841-23989364	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:23988838-23989639	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr3:23988757-23989457	K562	blood:	n/a	n/a
36	JUND	chr3:23988711-23989325	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr3:23985541-23990663	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:23988745-23989346	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr3:23988915-23989233	MCF10A-Er-Src	breast:	n/a	n/a
40	TEAD4	chr3:23988818-23989342	ECC-1	luminal epithelium:	n/a	n/a
41	MAFF	chr3:23988737-23989275	K562	blood:	n/a	n/a
42	POLR2A	chr3:23989186-23989429	H1-hESC	embryonic stem cell:	n/a	n/a
43	STAT3	chr3:23988688-23989276	MCF10A-Er-Src	breast:	n/a	chr3:23988824-23988832
44	NR2F2	chr3:23988625-23989867	K562	blood:	n/a	n/a
45	EP300	chr3:23988709-23989360	ECC-1	luminal epithelium:	n/a	n/a
46	FOSL2	chr3:23988698-23989416	SK-N-SH	brain:	n/a	n/a
47	RPC155	chr3:23989123-23989705	K562	blood:	n/a	n/a
48	CEBPB	chr3:23988560-23989334	Hela-S3	cervix:	n/a	n/a
49	RFX5	chr3:23988956-23989263	Hela-S3	cervix:	n/a	n/a
50	GATA2	chr3:23988670-23989350	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23988282..23990131-chr3:24033697..24035885,2	MCF-7	breast:
2	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
3	chr3:23988541..23991177-chr3:24537846..24539360,2	K562	blood:
4	chr3:23988335..23991846-chr3:24002543..24006084,3	K562	blood:
5	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
6	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11917128	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28510558	0.87[EUR][1000 genomes]
rs55824572	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57434897	0.87[AFR][1000 genomes]
rs73036778	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73036780	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23987800-23990000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:23987800-23991200	Enhancers	Fetal Heart	heart
3	chr3:23988000-23989400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:23988000-23989400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:23988000-23989400	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr3:23988000-23990000	Flanking Active TSS	K562	blood
7	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
8	chr3:23988200-23989400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:23988200-23989400	Weak transcription	Gastric	stomach
10	chr3:23988200-23989400	Weak transcription	Lung	lung
11	chr3:23988200-23990000	Enhancers	Left Ventricle	heart
12	chr3:23988200-23990000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:23988200-23990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:23988200-23991000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:23988200-23992200	Enhancers	Small Intestine	intestine
16	chr3:23988200-23992200	Enhancers	Stomach Mucosa	stomach
17	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
18	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
19	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:23988400-23989400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:23988400-23989400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:23988400-23989600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:23988400-23989600	Enhancers	Fetal Muscle Leg	muscle
24	chr3:23988400-23989800	Enhancers	Fetal Lung	lung
25	chr3:23988400-23989800	Enhancers	Placenta	Placenta
26	chr3:23988400-23990000	Enhancers	Fetal Intestine Small	intestine
27	chr3:23988400-23990200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:23988400-23990400	Enhancers	Duodenum Mucosa	Duodenum
29	chr3:23988400-23990800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:23988400-23991600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:23988400-23991600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:23988400-23991800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:23988400-23992400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
40	chr3:23988600-23989400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr3:23988600-23989400	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr3:23988600-23989400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr3:23988600-23989800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:23988600-23990600	Enhancers	Right Ventricle	heart
45	chr3:23988600-23991000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
47	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr3:23988800-23989400	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr3:23988800-23989600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:23988800-23989600	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links