Variant report

Variant	rs9866124
Chromosome Location	chr3:48597553-48597554
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48595520-48602478	A549	lung:	n/a	n/a
2	POLR2A	chr3:48597501-48597733	K562	blood:	n/a	n/a
3	POLR2A	chr3:48597551-48597659	MCF-7	breast:	n/a	n/a
4	RCOR1	chr3:48597497-48597881	HepG2	liver:	n/a	n/a
5	CTCF	chr3:48597540-48597690	WERI-Rb-1	eye:	n/a	n/a
6	CTCF	chr3:48597540-48597690	GM12865	blood:	n/a	n/a
7	MXI1	chr3:48593292-48599174	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:48597305-48601913	U87	brain:	n/a	n/a
9	RFX5	chr3:48597526-48597683	HepG2	liver:	n/a	n/a
10	MYBL2	chr3:48597326-48597957	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:48597367-48601913	U87	brain:	n/a	n/a
12	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
13	MAX	chr3:48597494-48599126	NB4	blood:	n/a	chr3:48598678-48598688
14	EP300	chr3:48597337-48597766	HepG2	liver:	n/a	n/a
15	CTCF	chr3:48597553-48597809	GM19239	blood:	n/a	n/a
16	POLR2A	chr3:48597411-48598068	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:48595475-48603087	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:48597551-48597708	A549	lung:	n/a	n/a
19	POLR2A	chr3:48592306-48602182	U87	brain:	n/a	n/a
20	MTA3	chr3:48597364-48598173	GM12878	blood:	n/a	n/a
21	BHLHE40	chr3:48597500-48597723	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:48597192-48599116	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48596333..48598381-chr3:48723382..48725322,2	K562	blood:
2	chr3:48596168..48597991-chr3:48701051..48702925,2	K562	blood:
3	chr3:48596986..48597558-chr3:48646558..48647435,2	MCF-7	breast:
4	chr3:48595781..48598456-chr3:48600840..48603060,2	MCF-7	breast:
5	chr3:48512815..48516100-chr3:48594601..48597600,3	K562	blood:
6	chr3:48596009..48598246-chr3:48600524..48602479,3	K562	blood:
7	chr3:48592800..48598084-chr3:48598125..48603493,9	MCF-7	breast:
8	chr3:48595714..48598614-chr3:48603888..48605538,2	MCF-7	breast:
9	chr3:48595024..48597915-chr3:48619806..48622273,2	K562	blood:

No data

Variant related genes	Relation type
PFKFB4	TF binding region
ENSG00000164054	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000145040	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000010256	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1387005	0.89[ASW][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes]
rs28391653	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4858794	1.00[TSI][hapmap]
rs55952796	0.81[AFR][1000 genomes]
rs59643945	0.82[AMR][1000 genomes]
rs61368683	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs73831583	0.80[AFR][1000 genomes]
rs9833600	0.89[ASW][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes]
rs9839959	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS 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	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48593600-48599000	Enhancers	Stomach Mucosa	stomach
2	chr3:48594600-48599200	Enhancers	Fetal Heart	heart
3	chr3:48594600-48599200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr3:48594800-48597600	Weak transcription	Gastric	stomach
5	chr3:48595000-48597600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48595000-48597600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:48595000-48597600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:48595000-48597800	Enhancers	NHDF-Ad	bronchial
9	chr3:48595000-48598000	Enhancers	Primary hematopoietic stem cells	blood
10	chr3:48595000-48598000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:48595000-48598000	Enhancers	Placenta	Placenta
12	chr3:48595000-48598200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:48595000-48598200	Enhancers	Right Ventricle	heart
14	chr3:48595000-48598800	Enhancers	Pancreas	Pancrea
15	chr3:48595000-48599200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:48595200-48597800	Weak transcription	Fetal Intestine Small	intestine
17	chr3:48595200-48597800	Enhancers	Fetal Muscle Trunk	muscle
18	chr3:48595200-48598000	Enhancers	Brain Cingulate Gyrus	brain
19	chr3:48595200-48598000	Enhancers	Fetal Stomach	stomach
20	chr3:48595200-48598000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:48595200-48598200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:48595200-48599000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:48595200-48599000	Enhancers	Fetal Thymus	thymus
24	chr3:48595400-48597600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:48595400-48597800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:48595400-48597800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:48595400-48597800	Enhancers	Colonic Mucosa	Colon
28	chr3:48595400-48597800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr3:48595400-48598000	Enhancers	Fetal Muscle Leg	muscle
30	chr3:48595400-48598200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:48595400-48598200	Enhancers	Brain Hippocampus Middle	brain
32	chr3:48595400-48602000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:48595600-48597600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:48595600-48597600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:48595600-48597600	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:48595600-48597600	Enhancers	Osteobl	bone
37	chr3:48595600-48597800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:48595600-48597800	Enhancers	GM12878-XiMat	blood
39	chr3:48595600-48597800	Enhancers	HSMM	muscle
40	chr3:48595600-48597800	Weak transcription	HUVEC	blood vessel
41	chr3:48595600-48598000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:48595600-48598000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:48595800-48597600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:48595800-48597600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:48595800-48597600	Enhancers	Duodenum Mucosa	Duodenum
46	chr3:48595800-48598000	Enhancers	HSMMtube	muscle
47	chr3:48595800-48599000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:48595800-48599000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:48595800-48599000	Flanking Active TSS	HepG2	liver
50	chr3:48595800-48599200	Enhancers	Brain Inferior Temporal Lobe	brain

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