Variant report

Variant	rs12416514
Chromosome Location	chr10:6183067-6183068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr10:6183017-6183982	SK-N-SH	brain:	n/a	n/a
2	NFIC	chr10:6182771-6184235	GM12878	blood:	n/a	n/a
3	TCF3	chr10:6183055-6183506	GM12878	blood:	n/a	n/a
4	MXI1	chr10:6182941-6184025	IMR90	lung:	n/a	n/a
5	FOXM1	chr10:6182764-6184342	GM12878	blood:	n/a	n/a
6	SP1	chr10:6183037-6183504	GM12878	blood:	n/a	n/a
7	RELA	chr10:6182915-6184102	GM18505	blood:	n/a	n/a
8	TCF12	chr10:6182957-6184001	SK-N-SH	brain:	n/a	n/a
9	MXI1	chr10:6182817-6184057	GM12878	blood:	n/a	n/a
10	PBX3	chr10:6183063-6183962	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr10:6182780-6184101	GM12878	blood:	n/a	n/a
12	BCLAF1	chr10:6182798-6184187	GM12878	blood:	n/a	n/a
13	ZNF143	chr10:6183025-6183702	GM12878	blood:	n/a	n/a
14	SPI1	chr10:6183047-6183664	GM12891	blood:	n/a	n/a
15	SPI1	chr10:6183060-6183570	GM12878	blood:	n/a	n/a
16	CHD1	chr10:6182777-6184233	IMR90	lung:	n/a	n/a
17	BCL11A	chr10:6182829-6184316	GM12878	blood:	n/a	n/a
18	JUND	chr10:6183005-6183809	SK-N-SH	brain:	n/a	chr10:6183319-6183331
19	EBF1	chr10:6182473-6184172	GM12878	blood:	n/a	n/a
20	CHD1	chr10:6182327-6184009	GM12878	blood:	n/a	n/a
21	POU2F2	chr10:6182966-6184125	GM12878	blood:	n/a	n/a
22	IRF4	chr10:6182862-6184208	GM12878	blood:	n/a	n/a
23	IKZF1	chr10:6182317-6184632	GM12878	blood:	n/a	n/a
24	MAZ	chr10:6182597-6184110	GM12878	blood:	n/a	n/a
25	JUND	chr10:6183037-6183834	SK-N-SH	brain:	n/a	chr10:6183319-6183331
26	RCOR1	chr10:6182943-6184039	GM12878	blood:	n/a	n/a
27	RUNX3	chr10:6182401-6184334	GM12878	blood:	n/a	chr10:6183700-6183709
28	SIN3AK20	chr10:6183059-6183756	SK-N-SH	brain:	n/a	n/a
29	RUNX3	chr10:6182319-6184374	GM12878	blood:	n/a	chr10:6183700-6183709
30	CHD2	chr10:6182498-6184022	GM12878	blood:	n/a	n/a
31	CEBPB	chr10:6183059-6183608	IMR90	lung:	n/a	n/a
32	RELA	chr10:6183017-6184337	GM12878	blood:	n/a	n/a
33	SPI1	chr10:6182514-6184066	GM12878	blood:	n/a	n/a
34	GATA3	chr10:6183064-6183873	MCF-7	breast:	n/a	n/a
35	ATF2	chr10:6182908-6184226	GM12878	blood:	n/a	n/a
36	RELA	chr10:6182936-6184311	GM18951	blood:	n/a	n/a
37	FOSL2	chr10:6183016-6183848	SK-N-SH	brain:	n/a	chr10:6183319-6183331
38	BHLHE40	chr10:6182477-6184159	GM12878	blood:	n/a	n/a
39	MAX	chr10:6182513-6184037	GM12878	blood:	n/a	n/a
40	EP300	chr10:6183039-6183994	GM12878	blood:	n/a	n/a
41	FOXM1	chr10:6182989-6183916	GM12878	blood:	n/a	n/a
42	RELA	chr10:6182910-6184190	GM19193	blood:	n/a	n/a
43	EP300	chr10:6182404-6184252	GM12878	blood:	n/a	chr10:6182450-6182460
44	EBF1	chr10:6182511-6184195	GM12878	blood:	n/a	n/a
45	BATF	chr10:6183032-6183954	GM12878	blood:	n/a	n/a
46	IRF4	chr10:6182860-6184134	GM12878	blood:	n/a	n/a
47	SIN3A	chr10:6182399-6183818	GM12878	blood:	n/a	chr10:6182646-6182659
48	PBX3	chr10:6183029-6183788	SK-N-SH	brain:	n/a	n/a
49	PAX5	chr10:6182919-6184174	GM12878	blood:	n/a	chr10:6183737-6183746
50	TBL1XR1	chr10:6183060-6184028	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6181525..6183322-chr10:6221078..6223708,2	MCF-7	breast:
2	chr10:6060947..6063701-chr10:6181512..6183483,2	K562	blood:
3	chr10:6182309..6185774-chr10:6185942..6188983,5	MCF-7	breast:
4	chr10:6171947..6174676-chr10:6182111..6184339,3	MCF-7	breast:
5	chr10:6182985..6185643-chr10:6203385..6205220,2	K562	blood:
6	chr10:6180971..6185195-chr10:6203384..6207419,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFKFB3-1	chr10:6183050-6183545	XLOC_008366

No data

Variant related genes	Relation type
PFKFB3	TF binding region
ENSG00000170525	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10905861	0.80[AMR][1000 genomes]
rs11256685	0.80[AMR][1000 genomes]
rs11256893	0.90[AMR][1000 genomes]
rs12264240	0.80[AMR][1000 genomes]
rs12412910	0.80[AMR][1000 genomes]
rs13376791	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv894816	chr10:6173416-6190343	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv894817	chr10:6173416-6251252	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6171400-6183200	Weak transcription	Right Atrium	heart
2	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:6180600-6183400	Weak transcription	Esophagus	oesophagus
4	chr10:6181600-6183200	Enhancers	Fetal Thymus	thymus
5	chr10:6181600-6183600	Enhancers	Spleen	Spleen
6	chr10:6181600-6184000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:6181800-6183600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:6182000-6183200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:6182000-6183200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr10:6182000-6183400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:6182000-6183400	Enhancers	Psoas Muscle	Psoas
12	chr10:6182000-6183600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr10:6182000-6183800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr10:6182000-6184000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:6182000-6184400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr10:6182000-6185400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:6182200-6183200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr10:6182200-6183600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr10:6182200-6183600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr10:6182200-6184000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
21	chr10:6182200-6184000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr10:6182200-6184000	Flanking Active TSS	GM12878-XiMat	blood
23	chr10:6182400-6183200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr10:6182400-6183200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:6182400-6183200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr10:6182400-6183200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr10:6182400-6183200	Enhancers	Liver	Liver
28	chr10:6182400-6183200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr10:6182400-6183200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr10:6182400-6183200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr10:6182400-6183400	Enhancers	Brain Anterior Caudate	brain
32	chr10:6182400-6183400	Flanking Active TSS	HSMMtube	muscle
33	chr10:6182400-6183600	Active TSS	Rectal Smooth Muscle	rectum
34	chr10:6182400-6184000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr10:6182400-6184000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
36	chr10:6182400-6184000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
37	chr10:6182400-6184000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr10:6182400-6184000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr10:6182400-6184000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr10:6182400-6184200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr10:6182400-6184200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:6182600-6183200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr10:6182600-6183200	Bivalent Enhancer	Placenta	Placenta
44	chr10:6182600-6183200	Flanking Active TSS	HSMM	muscle
45	chr10:6182600-6183200	Bivalent Enhancer	K562	blood
46	chr10:6182600-6183400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:6182600-6183600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr10:6182600-6183600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:6182600-6184000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr10:6182600-6185000	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links