Variant report

Variant	rs57046386
Chromosome Location	chr3:53197420-53197421
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	CHD2	chr3:53195384-53197613	GM12878	blood:	n/a	chr3:53196018-53196028
2	ELF1	chr3:53196741-53197498	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:53196893-53197537	GM18951	blood:	n/a	n/a
4	POU2F2	chr3:53196138-53197641	GM12878	blood:	n/a	chr3:53197328-53197340 chr3:53196280-53196292 chr3:53197160-53197172
5	WRNIP1	chr3:53196469-53198198	GM12878	blood:	n/a	n/a
6	BCLAF1	chr3:53196279-53197578	GM12878	blood:	n/a	n/a
7	NFATC1	chr3:53196676-53197685	GM12878	blood:	n/a	n/a
8	EBF1	chr3:53195877-53198088	GM12878	blood:	n/a	chr3:53196035-53196044 chr3:53198051-53198064 chr3:53196997-53197006 chr3:53198053-53198062 chr3:53196034-53196045
9	PAX5	chr3:53196949-53197479	GM12878	blood:	n/a	n/a
10	MYC	chr3:53197165-53197434	GM12878	blood:	n/a	n/a
11	RUNX3	chr3:53196899-53197659	GM12878	blood:	n/a	n/a
12	EBF1	chr3:53197011-53197586	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:53194482-53198512	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:53194588-53197470	GM19099	blood:	n/a	n/a
15	MTA3	chr3:53197129-53197630	GM12878	blood:	n/a	n/a
16	EGR1	chr3:53197112-53197469	GM12878	blood:	n/a	chr3:53197311-53197322 chr3:53197304-53197317 chr3:53197330-53197344 chr3:53197310-53197323 chr3:53197311-53197325 chr3:53197313-53197322 chr3:53197310-53197323 chr3:53197310-53197324
17	CEBPB	chr3:53197216-53197450	GM12878	blood:	n/a	n/a
18	SIN3A	chr3:53196080-53197606	GM12878	blood:	n/a	n/a
19	SPI1	chr3:53197044-53197495	GM12891	blood:	n/a	n/a
20	NFIC	chr3:53197012-53197570	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:53194575-53197885	GM18505	blood:	n/a	n/a
22	STAT5A	chr3:53196136-53198360	GM12878	blood:	n/a	chr3:53197773-53197781 chr3:53196376-53196388
23	MAZ	chr3:53195502-53197515	GM12878	blood:	n/a	chr3:53196435-53196445 chr3:53195952-53195962
24	POLR2A	chr3:53196948-53197465	GM12891	blood:	n/a	n/a
25	POLR2A	chr3:53194684-53197963	GM12878	blood:	n/a	n/a
26	RELA	chr3:53196266-53197773	GM10847	blood:	n/a	n/a
27	TBP	chr3:53197052-53197541	GM12878	blood:	n/a	n/a
28	POLR2A	chr3:53194594-53197853	GM12878	blood:	n/a	n/a
29	MAX	chr3:53195682-53197734	NB4	blood:	n/a	chr3:53197434-53197444 chr3:53196435-53196445 chr3:53195952-53195962
30	POLR2A	chr3:53196927-53197466	GM12878	blood:	n/a	n/a
31	TEAD4	chr3:53197136-53197529	K562	blood:	n/a	n/a
32	MAX	chr3:53197264-53197613	K562	blood:	n/a	chr3:53197434-53197444
33	ATF2	chr3:53196862-53197582	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:53194621-53197512	GM12878	blood:	n/a	n/a
35	MAX	chr3:53196432-53197684	GM12878	blood:	n/a	chr3:53197434-53197444 chr3:53196435-53196445
36	MTA3	chr3:53195870-53198014	GM12878	blood:	n/a	n/a
37	SPI1	chr3:53197154-53197462	GM12878	blood:	n/a	n/a
38	BHLHE40	chr3:53197294-53197421	K562	blood:	n/a	n/a
39	POLR2A	chr3:53196976-53197561	HL-60	blood:	n/a	n/a
40	HDAC2	chr3:53197162-53197443	K562	blood:	n/a	n/a
41	POLR2A	chr3:53196963-53197557	GM12891	blood:	n/a	n/a
42	BHLHE40	chr3:53195981-53197637	GM12878	blood:	n/a	n/a
43	BCLAF1	chr3:53196262-53197619	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:53194614-53197550	GM12878	blood:	n/a	n/a
45	EGR1	chr3:53197161-53197522	GM12878	blood:	n/a	chr3:53197311-53197322 chr3:53197304-53197317 chr3:53197330-53197344 chr3:53197310-53197323 chr3:53197311-53197325 chr3:53197313-53197322 chr3:53197310-53197323 chr3:53197310-53197324
46	POLR2A	chr3:53194464-53197543	GM19193	blood:	n/a	n/a
47	STAT5A	chr3:53197128-53197841	GM12878	blood:	n/a	chr3:53197773-53197781
48	POLR2A	chr3:53194608-53197593	GM12878	blood:	n/a	n/a
49	EGR1	chr3:53197139-53197551	GM12878	blood:	n/a	chr3:53197311-53197322 chr3:53197304-53197317 chr3:53197330-53197344 chr3:53197310-53197323 chr3:53197311-53197325 chr3:53197313-53197322 chr3:53197310-53197323 chr3:53197310-53197324
50	POLR2A	chr3:53196798-53197520	GM12891	blood:	n/a	n/a

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: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11924565	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1483185	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1483186	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1483187	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242305	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3773724	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3773726	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3773727	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3773731	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3773733	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4687571	0.80[ASN][1000 genomes]
rs62254282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775022	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6797662	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6807359	0.83[EUR][1000 genomes]
rs72537447	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7630325	0.89[AMR][1000 genomes];0.86[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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196000-53197600	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr3:53196200-53197600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr3:53196200-53197600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr3:53196200-53198000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:53196200-53198000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr3:53196200-53198000	Enhancers	Fetal Heart	heart
7	chr3:53196400-53197600	Flanking Active TSS	Esophagus	oesophagus
8	chr3:53196400-53197800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:53196400-53197800	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr3:53196400-53198000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:53196400-53198000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:53196400-53198000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:53196400-53199200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr3:53196400-53202000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
16	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
17	chr3:53196600-53197600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:53196600-53197600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:53196600-53197600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr3:53196600-53197800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr3:53196600-53198000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:53196600-53198000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:53196600-53198200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:53196600-53199800	Weak transcription	Brain Germinal Matrix	brain
25	chr3:53196600-53200000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:53196600-53204000	Weak transcription	Small Intestine	intestine
27	chr3:53196800-53197600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:53196800-53197600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr3:53196800-53197600	Enhancers	Right Ventricle	heart
30	chr3:53196800-53197600	Flanking Active TSS	GM12878-XiMat	blood
31	chr3:53196800-53197800	Enhancers	A549	lung
32	chr3:53196800-53197800	Enhancers	K562	blood
33	chr3:53196800-53198000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:53196800-53199400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr3:53197000-53197600	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr3:53197000-53197600	Flanking Active TSS	Stomach Mucosa	stomach
37	chr3:53197000-53197600	Flanking Active TSS	HepG2	liver
38	chr3:53197000-53197800	Flanking Active TSS	Fetal Intestine Large	intestine
39	chr3:53197000-53197800	Enhancers	Thymus	Thymus
40	chr3:53197000-53198000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr3:53197000-53198000	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:53197000-53198000	Enhancers	Fetal Muscle Trunk	muscle
43	chr3:53197000-53198000	Enhancers	Fetal Muscle Leg	muscle
44	chr3:53197000-53198200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:53197000-53200400	Weak transcription	Liver	Liver
46	chr3:53197000-53200400	Weak transcription	HSMMtube	muscle
47	chr3:53197000-53202000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:53197200-53197600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:53197200-53197600	Enhancers	Primary T cells from cord blood	blood
50	chr3:53197200-53197600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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