Variant report

Variant	rs28430452
Chromosome Location	chr4:53524939-53524940
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	YY1	chr4:53524914-53526431	SK-N-SH	brain:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
2	MAZ	chr4:53524907-53524987	HepG2	liver:	n/a	n/a
3	YY1	chr4:53524890-53526329	HepG2	liver:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
4	POLR2A	chr4:53524888-53525834	HEK293	kidney:	n/a	n/a
5	POLR2A	chr4:53524897-53526532	GM18505	blood:	n/a	n/a
6	HCFC1	chr4:53524899-53525730	K562	blood:	n/a	n/a
7	TAF1	chr4:53524882-53526269	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr4:53524695-53525998	ECC-1	luminal epithelium:	n/a	n/a
9	POLR2A	chr4:53524926-53526430	GM12892	blood:	n/a	n/a
10	EBF1	chr4:53524783-53525011	GM12878	blood:	n/a	chr4:53524955-53524964
11	ZBTB7A	chr4:53524780-53525412	K562	blood:	n/a	n/a
12	SMARCB1	chr4:53524913-53526553	Hela-S3	cervix:	n/a	n/a
13	YY1	chr4:53524832-53526303	GM12892	blood:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
14	POLR2A	chr4:53524885-53526430	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZBTB7A	chr4:53524795-53525639	ECC-1	luminal epithelium:	n/a	n/a
16	MAZ	chr4:53524810-53526566	K562	blood:	n/a	chr4:53525015-53525025
17	UBTF	chr4:53524736-53526447	K562	blood:	n/a	n/a
18	YY1	chr4:53524896-53525755	GM12891	blood:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525105-53525116 chr4:53525343-53525355 chr4:53525344-53525366
19	MAZ	chr4:53524846-53526277	GM12878	blood:	n/a	chr4:53525015-53525025
20	MAX	chr4:53524840-53525126	K562	blood:	n/a	chr4:53525015-53525025
21	RUNX3	chr4:53524687-53525496	GM12878	blood:	n/a	n/a
22	REST	chr4:53524810-53526314	H1-neurons	neurons:	n/a	chr4:53526098-53526111
23	HA-E2F1	chr4:53524920-53526378	Hela-S3	cervix:	n/a	chr4:53526361-53526368 chr4:53526361-53526368 chr4:53525403-53525413 chr4:53525948-53525958 chr4:53526361-53526368
24	POLR2A	chr4:53524913-53526294	NB4	blood:	n/a	n/a
25	EBF1	chr4:53524750-53525092	GM12878	blood:	n/a	chr4:53524955-53524964
26	ZNF143	chr4:53524912-53526340	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:53524842-53526521	GM19099	blood:	n/a	n/a
28	POLR2A	chr4:53524762-53525982	H1-neurons	neurons:	n/a	n/a
29	ELF1	chr4:53524885-53526425	GM12878	blood:	n/a	chr4:53525405-53525414
30	MXI1	chr4:53523572-53526602	IMR90	lung:	n/a	n/a
31	POLR2A	chr4:53524829-53525900	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr4:53524903-53526273	GM18951	blood:	n/a	n/a
33	RUNX3	chr4:53524646-53525711	GM12878	blood:	n/a	n/a
34	TAF1	chr4:53524908-53525424	K562	blood:	n/a	n/a
35	MAZ	chr4:53524556-53526814	IMR90	lung:	n/a	chr4:53525015-53525025
36	SIN3A	chr4:53523707-53526506	H1-hESC	embryonic stem cell:	n/a	chr4:53526089-53526102 chr4:53525406-53525417 chr4:53525373-53525383
37	EGR1	chr4:53524887-53525524	K562	blood:	n/a	chr4:53524946-53524959 chr4:53525464-53525478 chr4:53525175-53525189 chr4:53525397-53525407
38	CCNT2	chr4:53524913-53526337	K562	blood:	n/a	chr4:53525976-53525985 chr4:53524945-53524954
39	CTCF	chr4:53524840-53524990	AG04449	skin:	n/a	n/a
40	TAF1	chr4:53524895-53526338	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr4:53524890-53525467	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:53524921-53526460	GM12878	blood:	n/a	n/a
43	ZBTB7A	chr4:53524815-53526226	K562	blood:	n/a	n/a
44	POLR2A	chr4:53523759-53526466	H1-hESC	embryonic stem cell:	n/a	n/a
45	YY1	chr4:53524892-53526202	GM12878	blood:	n/a	chr4:53525129-53525143 chr4:53525406-53525417 chr4:53526019-53526038 chr4:53525944-53525955 chr4:53525347-53525355 chr4:53525344-53525354 chr4:53525345-53525353 chr4:53525866-53525880 chr4:53525105-53525116 chr4:53525869-53525883 chr4:53525343-53525355 chr4:53525344-53525366
46	CHD2	chr4:53524896-53525793	GM12878	blood:	n/a	n/a
47	POLR2A	chr4:53524904-53526497	GM12878	blood:	n/a	n/a
48	HMGN3	chr4:53524881-53526319	K562	blood:	n/a	n/a
49	POLR2A	chr4:53524921-53525846	K562	blood:	n/a	n/a
50	POLR2A	chr4:53524903-53526866	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:53523849..53530507-chr4:53576531..53584814,17	K562	blood:
2	chr4:53524001..53527558-chr4:53577308..53580194,4	MCF-7	breast:
3	chr4:53519355..53522911-chr4:53523707..53526726,6	MCF-7	breast:
4	chr4:53523914..53526614-chr4:53586643..53588754,3	MCF-7	breast:
5	chr4:53492777..53495734-chr4:53523846..53526517,2	K562	blood:
6	chr4:53523968..53528771-chr4:53576572..53580241,9	MCF-7	breast:
7	chr4:53522789..53525024-chr4:53586830..53589438,2	K562	blood:
8	chr4:53515781..53522890-chr4:53523068..53527068,15	MCF-7	breast:
9	chr4:53522503..53529252-chr4:53576629..53581800,10	K562	blood:

Variant related genes	Relation type
USP46	TF binding region
USP46-AS1	TF binding region
ENSG00000226950	Chromatin interaction
ENSG00000212588	Chromatin interaction
ENSG00000248375	Chromatin interaction
ENSG00000109189	Chromatin interaction
ENSG00000264585	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10000311	1.00[ASN][1000 genomes]
rs10001085	0.93[ASN][1000 genomes]
rs10001370	0.87[ASN][1000 genomes]
rs10001387	0.93[ASN][1000 genomes]
rs10002261	0.90[ASN][1000 genomes]
rs10003396	0.87[ASN][1000 genomes]
rs10010306	0.93[ASN][1000 genomes]
rs10012676	0.87[ASN][1000 genomes]
rs10014752	1.00[ASN][1000 genomes]
rs10014850	0.94[ASN][1000 genomes]
rs10020568	0.90[ASN][1000 genomes]
rs10021143	0.93[ASN][1000 genomes]
rs10023867	0.93[ASN][1000 genomes]
rs10027906	0.90[ASN][1000 genomes]
rs10028085	0.90[ASN][1000 genomes]
rs10028755	0.90[ASN][1000 genomes]
rs10029145	0.93[ASN][1000 genomes]
rs10031386	1.00[ASN][1000 genomes]
rs10032700	1.00[ASN][1000 genomes]
rs10033218	1.00[ASN][1000 genomes]
rs10471216	1.00[ASN][1000 genomes]
rs13434726	0.87[ASN][1000 genomes]
rs13435157	0.87[ASN][1000 genomes]
rs17051569	0.83[AMR][1000 genomes]
rs17051587	0.83[AMR][1000 genomes]
rs17051645	0.83[AMR][1000 genomes]
rs28376189	0.90[ASN][1000 genomes]
rs28379922	0.90[ASN][1000 genomes]
rs28380682	0.93[ASN][1000 genomes]
rs28402205	1.00[ASN][1000 genomes]
rs28411005	1.00[ASN][1000 genomes]
rs28412170	0.93[ASN][1000 genomes]
rs28451750	0.93[ASN][1000 genomes]
rs28475600	0.93[ASN][1000 genomes]
rs28482298	0.93[ASN][1000 genomes]
rs28503210	0.93[ASN][1000 genomes]
rs28565016	0.93[ASN][1000 genomes]
rs28588481	0.94[ASN][1000 genomes]
rs28590396	1.00[ASN][1000 genomes]
rs28619184	0.93[ASN][1000 genomes]
rs28644292	0.93[ASN][1000 genomes]
rs28654693	1.00[ASN][1000 genomes]
rs28660550	1.00[ASN][1000 genomes]
rs28660571	1.00[ASN][1000 genomes]
rs28672279	0.93[ASN][1000 genomes]
rs28694544	0.90[ASN][1000 genomes]
rs28721897	1.00[ASN][1000 genomes]
rs28722174	0.93[ASN][1000 genomes]
rs28784684	1.00[ASN][1000 genomes]
rs28825181	0.90[ASN][1000 genomes]
rs28825412	1.00[ASN][1000 genomes]
rs28849759	1.00[ASN][1000 genomes]
rs28852068	1.00[ASN][1000 genomes]
rs2898678	0.83[AMR][1000 genomes]
rs6830833	1.00[ASN][1000 genomes]
rs7673679	0.90[ASN][1000 genomes]
rs9990686	1.00[ASN][1000 genomes]
rs9994643	1.00[ASN][1000 genomes]
rs9997863	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	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
9	esv3344129	chr4:53524220-53527168	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53518600-53525200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:53523000-53527000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:53523600-53525000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
4	chr4:53523600-53526400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr4:53523800-53525000	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr4:53523800-53525000	Flanking Active TSS	Fetal Muscle Leg	muscle
7	chr4:53523800-53525000	Flanking Active TSS	HepG2	liver
8	chr4:53523800-53526200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr4:53523800-53526400	Active TSS	Brain Angular Gyrus	brain
10	chr4:53523800-53526600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:53523800-53526600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:53523800-53526600	Active TSS	NHLF	lung
13	chr4:53523800-53526800	Active TSS	NHDF-Ad	bronchial
14	chr4:53523800-53527200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:53524000-53525000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr4:53524000-53525000	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr4:53524000-53525000	Flanking Active TSS	Dnd41	blood
18	chr4:53524000-53526200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:53524000-53526200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:53524000-53526200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:53524000-53526200	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:53524000-53526800	Active TSS	Aorta	Aorta
23	chr4:53524200-53525000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr4:53524200-53526000	Active TSS	Primary T cells from cord blood	blood
25	chr4:53524200-53526000	Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr4:53524200-53526200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:53524200-53526400	Active TSS	Fetal Kidney	kidney
28	chr4:53524200-53526600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr4:53524200-53526600	Active TSS	HSMMtube	muscle
30	chr4:53524400-53525000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr4:53524400-53525000	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr4:53524400-53525000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
33	chr4:53524400-53525000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr4:53524400-53526600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:53524400-53526600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr4:53524400-53526600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr4:53524600-53525000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr4:53524600-53525000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr4:53524600-53525000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr4:53524600-53525000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
41	chr4:53524600-53525000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:53524600-53525000	Flanking Active TSS	K562	blood
43	chr4:53524600-53525200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr4:53524600-53525200	Active TSS	Right Atrium	heart
45	chr4:53524600-53525400	Active TSS	Fetal Brain Male	brain
46	chr4:53524600-53525800	Active TSS	Brain Germinal Matrix	brain
47	chr4:53524600-53525800	Bivalent/Poised TSS	Thymus	Thymus
48	chr4:53524600-53526000	Active TSS	Fetal Stomach	stomach
49	chr4:53524600-53526200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:53524600-53526200	Active TSS	iPS-18 Cell Line	embryonic stem cell

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