Variant report

Variant	rs35632454
Chromosome Location	chr4:69241665-69241666
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	CTCF	chr4:69241566-69242112	HepG2	liver:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
2	RAD21	chr4:69241625-69242058	Hela-S3	cervix:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
3	RAD21	chr4:69241650-69242155	H1-hESC	embryonic stem cell:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
4	RAD21	chr4:69241473-69242217	HCT-116	colon:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
5	RAD21	chr4:69241592-69242085	A549	lung:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
6	RAD21	chr4:69241632-69242073	SK-N-SH_RA	brain:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
7	RAD21	chr4:69241477-69242249	MCF-7	breast:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
8	CTCF	chr4:69241665-69241988	K562	blood:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
9	NRF1	chr4:69241657-69242110	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr4:69241281-69242104	GM12878	blood:	n/a	chr4:69241346-69241354 chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
11	CTCF	chr4:69241629-69242164	A549	lung:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
12	CTCF	chr4:69241054-69242268	HCT-116	colon:	n/a	chr4:69241346-69241354 chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
13	CTCF	chr4:69241640-69242093	IMR90	lung:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
14	CTCF	chr4:69241608-69242038	HCT-116	colon:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
15	CTCF	chr4:69241197-69242059	K562	blood:	n/a	chr4:69241346-69241354 chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
16	SMC3	chr4:69241663-69242059	GM12878	blood:	n/a	chr4:69241823-69241837
17	RAD21	chr4:69241129-69242249	HCT-116	colon:	n/a	chr4:69241829-69241836 chr4:69241819-69241838 chr4:69241343-69241357
18	CTCF	chr4:69241664-69242023	K562	blood:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
19	RAD21	chr4:69241658-69242264	H1-hESC	embryonic stem cell:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
20	RAD21	chr4:69241639-69242116	H1-hESC	embryonic stem cell:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
21	CTCF	chr4:69241615-69242041	A549	lung:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
22	RAD21	chr4:69241656-69242043	HepG2	liver:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
23	SMC3	chr4:69241477-69242178	SK-N-SH	brain:	n/a	chr4:69241823-69241837
24	CTCF	chr4:69241137-69242259	A549	lung:	n/a	chr4:69241346-69241354 chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
25	RAD21	chr4:69241259-69242307	SK-N-SH	brain:	n/a	chr4:69241829-69241836 chr4:69241819-69241838 chr4:69241343-69241357
26	CTCF	chr4:69241664-69242018	K562	blood:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
27	CTCF	chr4:69241563-69242101	T-47D	breast:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
28	CTCF	chr4:69241660-69242072	ECC-1	luminal epithelium:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
29	RAD21	chr4:69241544-69242082	A549	lung:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
30	SMC3	chr4:69241377-69242083	Hela-S3	cervix:	n/a	chr4:69241823-69241837
31	RAD21	chr4:69241643-69242152	IMR90	lung:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
32	RAD21	chr4:69241578-69242154	MCF-7	breast:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
33	CTCF	chr4:69241435-69242320	SK-N-SH	brain:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
34	CBX3	chr4:69241617-69242163	HCT-116	colon:	n/a	n/a
35	USF2	chr4:69241652-69241924	GM12878	blood:	n/a	n/a
36	RAD21	chr4:69241565-69242119	ECC-1	luminal epithelium:	n/a	chr4:69241829-69241836 chr4:69241819-69241838
37	CTCF	chr4:69241603-69241985	A549	lung:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
38	CTCF	chr4:69241647-69242074	H1-hESC	embryonic stem cell:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
39	CTCF	chr4:69241510-69242210	MCF-7	breast:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
40	CTCF	chr4:69241560-69242054	MCF-7	breast:	n/a	chr4:69241822-69241838 chr4:69241816-69241837 chr4:69241826-69241834
41	RFX5	chr4:69241653-69242034	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:69212970..69215845-chr4:69239349..69242311,2	MCF-7	breast:
2	chr4:69215315..69216150-chr4:69241399..69242116,2	MCF-7	breast:
3	chr4:69143211..69145096-chr4:69239415..69241951,2	K562	blood:

Variant related genes	Relation type
MT2P1	TF binding region
ENSG00000083896	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11726194	0.85[ASN][1000 genomes]
rs11727878	0.83[ASN][1000 genomes]
rs13124352	0.85[ASN][1000 genomes]
rs13130430	0.85[ASN][1000 genomes]
rs1406694	0.93[ASN][1000 genomes]
rs17089267	0.82[ASN][1000 genomes]
rs1730873	0.82[ASN][1000 genomes]
rs1919898	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2319888	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2319891	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28656921	0.85[ASN][1000 genomes]
rs34419508	0.93[ASN][1000 genomes]
rs34452677	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34500620	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964416	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36098059	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36126120	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3797008	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428356	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6812178	0.82[ASN][1000 genomes]
rs7666993	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008084	chr4:68797598-69482831	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv537131	chr4:68797598-69482831	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1806586	chr4:68943858-69592846	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv537132	chr4:69149648-69482831	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2757061	chr4:69178920-69631668	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv437385	chr4:69204755-69383357	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv437386	chr4:69213885-69383357	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1006223	chr4:69217756-69540013	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv870075	chr4:69218674-69608683	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv3407776	chr4:69222857-69376755	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv3442208	chr4:69222907-69288205	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv879223	chr4:69223057-69592846	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv3397664	chr4:69223455-69592846	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3468149	chr4:69223455-69592846	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	esv3468150	chr4:69223455-69592846	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69232200-69255600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:69234200-69242000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:69235200-69242000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:69235400-69241800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:69235800-69243000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:69237400-69242000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:69239400-69241800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:69239400-69241800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr4:69239400-69241800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:69239400-69241800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:69239400-69241800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:69239400-69242000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr4:69239600-69241800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:69239600-69241800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:69239600-69241800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:69239600-69241800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:69239600-69241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:69239600-69241800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:69239600-69241800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:69239600-69241800	Weak transcription	Brain Hippocampus Middle	brain
21	chr4:69239600-69241800	Weak transcription	Esophagus	oesophagus
22	chr4:69239600-69241800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr4:69239600-69241800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:69239600-69241800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:69239600-69241800	Weak transcription	HSMM	muscle
26	chr4:69239600-69241800	Weak transcription	HSMMtube	muscle
27	chr4:69239600-69241800	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr4:69239600-69241800	Weak transcription	NH-A	brain
29	chr4:69239600-69242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:69239600-69242000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr4:69239600-69242000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr4:69239600-69242000	Weak transcription	Brain Substantia Nigra	brain
33	chr4:69239600-69242000	Weak transcription	Colonic Mucosa	Colon
34	chr4:69239600-69242000	Weak transcription	Psoas Muscle	Psoas
35	chr4:69239800-69241800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:69239800-69241800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:69239800-69241800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:69239800-69241800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:69239800-69241800	Weak transcription	Osteobl	bone
40	chr4:69240000-69245000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:69241200-69241800	Enhancers	H1 Cell Line	embryonic stem cell
42	chr4:69241200-69241800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr4:69241200-69241800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:69241200-69241800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:69241200-69241800	Enhancers	NHEK	skin
46	chr4:69241400-69241800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr4:69241400-69241800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr4:69241400-69241800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:69241400-69241800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:69241400-69241800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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