Variant report

Variant	rs73248690
Chromosome Location	chr4:53578309-53578310
allele	A/G
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	POLR2A	chr4:53578089-53583495	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:53578227-53579941	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr4:53577683-53579420	Raji	blood:	n/a	n/a
4	CHD1	chr4:53577918-53579564	IMR90	lung:	n/a	chr4:53578486-53578496
5	NR2F2	chr4:53578294-53579218	MCF-7	breast:	n/a	n/a
6	POLR2A	chr4:53578153-53579362	GM12878	blood:	n/a	n/a
7	ZNF143	chr4:53578036-53579308	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:53578148-53582137	HUVEC	blood vessel:	n/a	n/a
9	SP1	chr4:53578163-53578863	GM12878	blood:	n/a	chr4:53578555-53578567 chr4:53578555-53578567 chr4:53578486-53578498 chr4:53578487-53578497 chr4:53578486-53578498 chr4:53578555-53578566 chr4:53578487-53578496 chr4:53578488-53578497 chr4:53578444-53578453 chr4:53578486-53578497 chr4:53578487-53578496 chr4:53578556-53578565
10	MXI1	chr4:53578148-53579411	HepG2	liver:	n/a	n/a
11	JUN	chr4:53578303-53579595	K562	blood:	n/a	chr4:53578489-53578498 chr4:53578392-53578403
12	HMGN3	chr4:53578229-53579281	K562	blood:	n/a	n/a
13	MAX	chr4:53578068-53578775	K562	blood:	n/a	n/a
14	MYC	chr4:53578212-53580226	K562	blood:	n/a	chr4:53579174-53579184
15	MXI1	chr4:53578029-53580148	IMR90	lung:	n/a	n/a
16	POLR2A	chr4:53578205-53578419	GM12891	blood:	n/a	n/a
17	MXI1	chr4:53578209-53580263	K562	blood:	n/a	n/a
18	POLR2A	chr4:53578171-53579290	HCT-116	colon:	n/a	n/a
19	RELA	chr4:53577969-53579973	GM10847	blood:	n/a	n/a
20	PML	chr4:53577437-53582791	GM12878	blood:	n/a	n/a
21	USF2	chr4:53578140-53579424	GM12878	blood:	n/a	chr4:53578547-53578563 chr4:53579175-53579186 chr4:53578819-53578835
22	BCLAF1	chr4:53578135-53579416	GM12878	blood:	n/a	chr4:53578819-53578832
23	WRNIP1	chr4:53577982-53578344	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:53578197-53578884	HepG2	liver:	n/a	n/a
25	MYC	chr4:53577950-53581737	K562	blood:	n/a	chr4:53581252-53581262 chr4:53579174-53579184
26	POLR2A	chr4:53578152-53580554	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr4:53578163-53578928	A549	lung:	n/a	n/a
28	YY1	chr4:53578140-53578905	ECC-1	luminal epithelium:	n/a	chr4:53578549-53578563 chr4:53578548-53578562
29	POLR2A	chr4:53578182-53579417	GM12891	blood:	n/a	n/a
30	RAD21	chr4:53578292-53578754	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBL1XR1	chr4:53577841-53578312	K562	blood:	n/a	n/a
32	POLR2A	chr4:53577817-53585334	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr4:53578212-53579318	MCF-7	breast:	n/a	n/a
34	MAZ	chr4:53578227-53579363	Hela-S3	cervix:	n/a	n/a
35	MYC	chr4:53577799-53580031	NB4	blood:	n/a	chr4:53579174-53579184
36	CREB1	chr4:53578107-53579360	HepG2	liver:	n/a	n/a
37	ELF1	chr4:53578236-53579337	K562	blood:	n/a	n/a
38	POLR2A	chr4:53578182-53580055	GM10847	blood:	n/a	n/a
39	SIN3AK20	chr4:53578237-53579549	K562	blood:	n/a	n/a
40	YY1	chr4:53578193-53579266	GM12892	blood:	n/a	chr4:53578549-53578563 chr4:53578911-53578925 chr4:53578548-53578562
41	MAX	chr4:53578004-53579473	SK-N-SH	brain:	n/a	chr4:53579174-53579184
42	ZEB1	chr4:53578222-53579323	GM12878	blood:	n/a	chr4:53579120-53579133
43	SETDB1	chr4:53578180-53578703	U2OS	brain:	n/a	n/a
44	SIN3AK20	chr4:53577944-53579617	MCF-7	breast:	n/a	n/a
45	MAX	chr4:53577923-53579538	HCT-116	colon:	n/a	chr4:53579174-53579184
46	ZC3H11A	chr4:53578263-53578735	K562	blood:	n/a	n/a
47	MYC	chr4:53578097-53580444	K562	blood:	n/a	chr4:53579174-53579184
48	POLR2A	chr4:53577966-53580296	U87	brain:	n/a	n/a
49	E2F6	chr4:53578237-53578850	A549	lung:	n/a	n/a
50	HEY1	chr4:53578219-53578451	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53524001..53527558-chr4:53577308..53580194,4	MCF-7	breast:
2	chr4:53522503..53529252-chr4:53576629..53581800,10	K562	blood:
3	chr4:52708602..52710348-chr4:53576866..53578697,2	K562	blood:
4	chr4:53523968..53528771-chr4:53576572..53580241,9	MCF-7	breast:
5	chr4:53577786..53580191-chr4:53616571..53618498,3	K562	blood:
6	chr4:52708848..52711921-chr4:53577027..53578697,3	K562	blood:
7	chr4:53530807..53532670-chr4:53576832..53578474,2	K562	blood:
8	chr17:56736053..56736866-chr4:53578187..53579262,3	HCT-116	colon:
9	chr4:53523849..53530507-chr4:53576531..53584814,17	K562	blood:
10	chr4:53577642..53581381-chr4:53614382..53619478,5	MCF-7	breast:
11	chr4:53577014..53579334-chr4:54455969..54458582,2	K562	blood:
12	chr4:53577401..53580169-chr4:53726393..53730142,5	MCF-7	breast:

Variant related genes	Relation type
SNORA26	TF binding region
MIR4449	TF binding region
DANCR	TF binding region
ENSG00000109189	Chromatin interaction
ENSG00000128045	Chromatin interaction
ENSG00000248866	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000226887	Chromatin interaction
ENSG00000072201	Chromatin interaction
ENSG00000266656	Chromatin interaction
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17699414	1.00[AFR][1000 genomes]
rs73248668	1.00[AFR][1000 genomes]
rs73248683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73250912	1.00[AFR][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1005869	chr4:53571901-53649247	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53558200-53578600	Weak transcription	Aorta	Aorta
2	chr4:53576800-53578400	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:53577400-53578400	Flanking Active TSS	K562	blood
4	chr4:53577400-53578600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr4:53577600-53578400	Flanking Active TSS	Stomach Mucosa	stomach
6	chr4:53577600-53578400	Flanking Active TSS	NHEK	skin
7	chr4:53577600-53579400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr4:53577600-53579600	Active TSS	A549	lung
9	chr4:53577800-53578400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
10	chr4:53577800-53578400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:53577800-53578400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr4:53577800-53578400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr4:53577800-53579400	Active TSS	H9 Cell Line	embryonic stem cell
14	chr4:53577800-53579400	Active TSS	Brain Cingulate Gyrus	brain
15	chr4:53577800-53579600	Active TSS	Brain Angular Gyrus	brain
16	chr4:53577800-53579600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:53577800-53579600	Active TSS	Fetal Kidney	kidney
18	chr4:53578000-53578400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:53578000-53578400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr4:53578000-53578400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr4:53578000-53578400	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr4:53578000-53578400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr4:53578000-53578400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr4:53578000-53578400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:53578000-53578400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:53578000-53578400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
27	chr4:53578000-53578400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr4:53578000-53578400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:53578000-53578400	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr4:53578000-53578400	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr4:53578000-53578400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr4:53578000-53578400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr4:53578000-53578400	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr4:53578000-53578400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr4:53578000-53578400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr4:53578000-53578400	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr4:53578000-53578400	Flanking Active TSS	Dnd41	blood
38	chr4:53578000-53578400	Flanking Active TSS	Hela-S3	cervix
39	chr4:53578000-53578400	Flanking Active TSS	HepG2	liver
40	chr4:53578000-53578400	Flanking Active TSS	HUVEC	blood vessel
41	chr4:53578000-53578400	Flanking Active TSS	NH-A	brain
42	chr4:53578000-53578400	Flanking Active TSS	Osteobl	bone
43	chr4:53578000-53578600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:53578000-53578600	Enhancers	Spleen	Spleen
45	chr4:53578000-53578800	Active TSS	Brain Germinal Matrix	brain
46	chr4:53578000-53579000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr4:53578000-53579200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:53578000-53579200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:53578000-53579200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr4:53578000-53579200	Active TSS	Brain Anterior Caudate	brain

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