Variant report

Variant	rs4750016
Chromosome Location	chr10:6183805-6183806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:86)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:86 , 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	MEF2A	chr10:6183073-6183865	GM12878	blood:	n/a	n/a
3	MAX	chr10:6183153-6183869	MCF-7	breast:	n/a	n/a
4	CEBPB	chr10:6183069-6183922	GM12878	blood:	n/a	n/a
5	KAP1	chr10:6183462-6183964	U2OS	brain:	n/a	n/a
6	MAFK	chr10:6183114-6184001	IMR90	lung:	n/a	n/a
7	NFIC	chr10:6182771-6184235	GM12878	blood:	n/a	n/a
8	MXI1	chr10:6182941-6184025	IMR90	lung:	n/a	n/a
9	FOXM1	chr10:6182764-6184342	GM12878	blood:	n/a	n/a
10	MAX	chr10:6183095-6183820	SK-N-SH	brain:	n/a	n/a
11	MAZ	chr10:6183107-6183941	K562	blood:	n/a	n/a
12	RELA	chr10:6182915-6184102	GM18505	blood:	n/a	n/a
13	TCF12	chr10:6182957-6184001	SK-N-SH	brain:	n/a	n/a
14	MXI1	chr10:6182817-6184057	GM12878	blood:	n/a	n/a
15	PBX3	chr10:6183063-6183962	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr10:6182780-6184101	GM12878	blood:	n/a	n/a
17	BCLAF1	chr10:6182798-6184187	GM12878	blood:	n/a	n/a
18	CHD1	chr10:6182777-6184233	IMR90	lung:	n/a	n/a
19	CUX1	chr10:6183114-6184085	GM12878	blood:	n/a	n/a
20	BCL11A	chr10:6182829-6184316	GM12878	blood:	n/a	n/a
21	MAX	chr10:6183082-6183864	A549	lung:	n/a	n/a
22	JUND	chr10:6183005-6183809	SK-N-SH	brain:	n/a	chr10:6183319-6183331
23	EBF1	chr10:6182473-6184172	GM12878	blood:	n/a	n/a
24	E2F6	chr10:6183356-6183859	K562	blood:	n/a	n/a
25	CHD1	chr10:6182327-6184009	GM12878	blood:	n/a	n/a
26	POU2F2	chr10:6182966-6184125	GM12878	blood:	n/a	n/a
27	IRF4	chr10:6182862-6184208	GM12878	blood:	n/a	n/a
28	POLR2A	chr10:6183522-6183821	U87	brain:	n/a	n/a
29	IKZF1	chr10:6182317-6184632	GM12878	blood:	n/a	n/a
30	MAZ	chr10:6182597-6184110	GM12878	blood:	n/a	n/a
31	JUND	chr10:6183037-6183834	SK-N-SH	brain:	n/a	chr10:6183319-6183331
32	RCOR1	chr10:6182943-6184039	GM12878	blood:	n/a	n/a
33	RUNX3	chr10:6182401-6184334	GM12878	blood:	n/a	chr10:6183700-6183709
34	RUNX3	chr10:6182319-6184374	GM12878	blood:	n/a	chr10:6183700-6183709
35	ZNF384	chr10:6183115-6184345	GM12878	blood:	n/a	n/a
36	CHD2	chr10:6182498-6184022	GM12878	blood:	n/a	n/a
37	RELA	chr10:6183017-6184337	GM12878	blood:	n/a	n/a
38	SPI1	chr10:6182514-6184066	GM12878	blood:	n/a	n/a
39	JUND	chr10:6183135-6183848	GM12878	blood:	n/a	chr10:6183319-6183331
40	GATA3	chr10:6183064-6183873	MCF-7	breast:	n/a	n/a
41	ATF2	chr10:6182908-6184226	GM12878	blood:	n/a	n/a
42	RELA	chr10:6182936-6184311	GM18951	blood:	n/a	n/a
43	FOSL2	chr10:6183016-6183848	SK-N-SH	brain:	n/a	chr10:6183319-6183331
44	BCL3	chr10:6183637-6184202	GM12878	blood:	n/a	n/a
45	BHLHE40	chr10:6182477-6184159	GM12878	blood:	n/a	n/a
46	MAX	chr10:6183115-6183826	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr10:6183717-6184086	GM12878	blood:	n/a	n/a
48	MAX	chr10:6182513-6184037	GM12878	blood:	n/a	n/a
49	EP300	chr10:6183039-6183994	GM12878	blood:	n/a	n/a
50	FOXM1	chr10:6182989-6183916	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6183735..6189299-chr10:6241759..6246920,10	MCF-7	breast:
2	chr10:6182309..6185774-chr10:6185942..6188983,5	MCF-7	breast:
3	chr10:6171947..6174676-chr10:6182111..6184339,3	MCF-7	breast:
4	chr10:6182985..6185643-chr10:6203385..6205220,2	K562	blood:
5	chr10:6180971..6185195-chr10:6203384..6207419,4	MCF-7	breast:

No data

Variant related genes	Relation type
PFKFB3	TF binding region
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10400124	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10400125	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10400165	0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11256954	0.81[ASN][1000 genomes]
rs12218872	0.82[ASN][1000 genomes]
rs12219621	0.81[ASN][1000 genomes]
rs12219630	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12571538	0.81[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs3920615	0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs4747887	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4747888	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4750012	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4750015	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099083	0.82[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7476043	0.81[ASN][1000 genomes]
rs943121	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv437656	chr10:6183805-6189362	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4750016	PFKP	cis	cerebellum	SCAN
rs4750016	PFKP	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6176600-6185000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:6181600-6184000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr10:6182000-6184000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:6182000-6184400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr10:6182000-6185400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:6182200-6184000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:6182200-6184000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr10:6182200-6184000	Flanking Active TSS	GM12878-XiMat	blood
9	chr10:6182400-6184000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
10	chr10:6182400-6184000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
11	chr10:6182400-6184000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:6182400-6184000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr10:6182400-6184000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr10:6182400-6184000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr10:6182400-6184200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr10:6182400-6184200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr10:6182600-6184000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr10:6182600-6185000	Enhancers	Placenta Amnion	Placenta Amnion
19	chr10:6182800-6184000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr10:6182800-6186200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:6183000-6184000	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr10:6183000-6184000	Active TSS	Colonic Mucosa	Colon
23	chr10:6183000-6184000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr10:6183000-6184000	Active TSS	Stomach Smooth Muscle	stomach
25	chr10:6183000-6184000	Flanking Active TSS	NH-A	brain
26	chr10:6183000-6184200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr10:6183000-6184400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:6183000-6185000	Weak transcription	Primary B cells from cord blood	blood
29	chr10:6183000-6185200	Weak transcription	Pancreas	Pancrea
30	chr10:6183000-6185400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr10:6183000-6185800	Weak transcription	Primary T cells from cord blood	blood
32	chr10:6183000-6186000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:6183000-6186200	Weak transcription	Brain Angular Gyrus	brain
34	chr10:6183000-6186200	Weak transcription	HUVEC	blood vessel
35	chr10:6183200-6184000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr10:6183200-6184000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr10:6183200-6184000	Active TSS	NHDF-Ad	bronchial
38	chr10:6183200-6185600	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr10:6183200-6185600	Weak transcription	Fetal Thymus	thymus
40	chr10:6183200-6185600	Weak transcription	Dnd41	blood
41	chr10:6183200-6185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr10:6183400-6184000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
43	chr10:6183400-6184000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr10:6183400-6184000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:6183400-6184000	Active TSS	Aorta	Aorta
46	chr10:6183400-6184000	Active TSS	Brain Anterior Caudate	brain
47	chr10:6183400-6184000	Flanking Active TSS	K562	blood
48	chr10:6183400-6184000	Flanking Active TSS	NHLF	lung
49	chr10:6183400-6184200	Active TSS	Psoas Muscle	Psoas
50	chr10:6183400-6185000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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