Variant report

Variant	rs11924565
Chromosome Location	chr3:53197640-53197641
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	POU2F2	chr3:53196138-53197641	GM12878	blood:	n/a	chr3:53197328-53197340 chr3:53196280-53196292 chr3:53197160-53197172
2	WRNIP1	chr3:53196469-53198198	GM12878	blood:	n/a	n/a
3	NFATC1	chr3:53196676-53197685	GM12878	blood:	n/a	n/a
4	EBF1	chr3:53195877-53198088	GM12878	blood:	n/a	chr3:53196035-53196044 chr3:53198051-53198064 chr3:53196997-53197006 chr3:53198053-53198062 chr3:53196034-53196045
5	RUNX3	chr3:53196899-53197659	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:53194482-53198512	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:53194575-53197885	GM18505	blood:	n/a	n/a
8	STAT5A	chr3:53196136-53198360	GM12878	blood:	n/a	chr3:53197773-53197781 chr3:53196376-53196388
9	POLR2A	chr3:53194684-53197963	GM12878	blood:	n/a	n/a
10	RELA	chr3:53196266-53197773	GM10847	blood:	n/a	n/a
11	POLR2A	chr3:53194594-53197853	GM12878	blood:	n/a	n/a
12	MAX	chr3:53195682-53197734	NB4	blood:	n/a	chr3:53197434-53197444 chr3:53196435-53196445 chr3:53195952-53195962
13	MAX	chr3:53196432-53197684	GM12878	blood:	n/a	chr3:53197434-53197444 chr3:53196435-53196445
14	MTA3	chr3:53195870-53198014	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:53197600-53197800	K562	blood:	n/a	n/a
16	STAT5A	chr3:53197128-53197841	GM12878	blood:	n/a	chr3:53197773-53197781
17	POLR2A	chr3:53195933-53198350	GM12878	blood:	n/a	n/a
18	RUNX3	chr3:53196140-53197644	GM12878	blood:	n/a	n/a
19	MXI1	chr3:53197502-53197702	Hela-S3	cervix:	n/a	n/a
20	IRF4	chr3:53196139-53197646	GM12878	blood:	n/a	n/a
21	PML	chr3:53196169-53197742	GM12878	blood:	n/a	n/a
22	MXI1	chr3:53195940-53197812	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:53193966-53197708	GM12891	blood:	n/a	n/a
24	RELA	chr3:53196991-53197697	GM19099	blood:	n/a	n/a
25	CHD1	chr3:53195967-53197700	GM12878	blood:	n/a	chr3:53196018-53196028

No.	Distal block	Cell Line	Cell type
1	chr3:53196507..53199069-chr3:53217529..53219666,3	K562	blood:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53196633..53198963-chr3:53206853..53208584,2	K562	blood:
4	chr3:53163122..53165133-chr3:53195998..53198976,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000163933	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11130347	0.80[ASN][1000 genomes]
rs1483185	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1483186	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1483187	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3773724	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3773726	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3773727	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3773731	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3773733	0.87[ASN][1000 genomes]
rs4687571	0.82[ASN][1000 genomes]
rs57046386	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62254282	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6775022	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6797662	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6807359	0.83[EUR][1000 genomes]
rs72537447	0.82[AMR][1000 genomes];0.87[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	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196200-53198000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:53196200-53198000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr3:53196200-53198000	Enhancers	Fetal Heart	heart
4	chr3:53196400-53197800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:53196400-53197800	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr3:53196400-53198000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53196400-53198000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:53196400-53198000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:53196400-53199200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr3:53196400-53202000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
12	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
13	chr3:53196600-53197800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr3:53196600-53198000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:53196600-53198000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:53196600-53198200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:53196600-53199800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:53196600-53200000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:53196600-53204000	Weak transcription	Small Intestine	intestine
20	chr3:53196800-53197800	Enhancers	A549	lung
21	chr3:53196800-53197800	Enhancers	K562	blood
22	chr3:53196800-53198000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:53196800-53199400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr3:53197000-53197800	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr3:53197000-53197800	Enhancers	Thymus	Thymus
26	chr3:53197000-53198000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:53197000-53198000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr3:53197000-53198000	Enhancers	Fetal Muscle Trunk	muscle
29	chr3:53197000-53198000	Enhancers	Fetal Muscle Leg	muscle
30	chr3:53197000-53198200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:53197000-53200400	Weak transcription	Liver	Liver
32	chr3:53197000-53200400	Weak transcription	HSMMtube	muscle
33	chr3:53197000-53202000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:53197200-53197800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr3:53197200-53197800	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:53197200-53197800	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr3:53197200-53197800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr3:53197200-53197800	Enhancers	NHLF	lung
39	chr3:53197200-53198000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:53197200-53198000	Enhancers	Primary T cells fromperipheralblood	blood
41	chr3:53197200-53198000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
42	chr3:53197200-53198000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:53197200-53198000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr3:53197200-53198000	Enhancers	Osteobl	bone
45	chr3:53197200-53198400	Weak transcription	Fetal Thymus	thymus
46	chr3:53197200-53198800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:53197200-53199800	Weak transcription	NH-A	brain
48	chr3:53197200-53200200	Weak transcription	HUVEC	blood vessel
49	chr3:53197200-53200400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:53197200-53200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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