Variant report

Variant	rs531421581
Chromosome Location	chr3:140769988-140769989
allele	C/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	chr3:140769988-140770107	Fibrobl	skin:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
2	RAD21	chr3:140769669-140772103	SK-N-SH	brain:	n/a	chr3:140770060-140770072 chr3:140770036-140770055 chr3:140770040-140770054 chr3:140770536-140770546 chr3:140771703-140771722 chr3:140770334-140770344
3	MAX	chr3:140769500-140770400	NB4	blood:	n/a	chr3:140769762-140769772 chr3:140769811-140769818 chr3:140769810-140769819
4	CTCF	chr3:140769880-140770030	HRE	kidney:	n/a	n/a
5	CTCF	chr3:140769960-140770110	HUVEC	blood vessel:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
6	HA-E2F1	chr3:140769455-140770866	MCF-7	breast:	n/a	chr3:140769662-140769674 chr3:140770035-140770047 chr3:140770014-140770023 chr3:140769826-140769837 chr3:140770747-140770757 chr3:140769988-140769997 chr3:140770744-140770754 chr3:140770067-140770077
7	YY1	chr3:140769902-140770133	HCT-116	colon:	n/a	chr3:140770069-140770083 chr3:140769991-140770000 chr3:140770066-140770080 chr3:140770066-140770075 chr3:140769988-140769997 chr3:140770011-140770025 chr3:140770063-140770077
8	CTCF	chr3:140769951-140770139	MCF-7	breast:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
9	CTCF	chr3:140769980-140770130	MCF-7	breast:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
10	CTCF	chr3:140769801-140770277	H1-hESC	embryonic stem cell:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
11	CTCF	chr3:140769790-140770277	H1-hESC	embryonic stem cell:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
12	EP300	chr3:140769862-140770468	ECC-1	luminal epithelium:	n/a	chr3:140770370-140770386 chr3:140770014-140770023 chr3:140770068-140770077 chr3:140770066-140770075
13	CTCF	chr3:140769960-140770110	GM12867	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
14	CTCF	chr3:140769971-140770132	Gliobla	brain:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
15	CTCF	chr3:140769920-140770070	RPTEC	kidney:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
16	CTCF	chr3:140769980-140770130	GM12868	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
17	MAX	chr3:140769490-140770363	H1-hESC	embryonic stem cell:	n/a	chr3:140769762-140769772 chr3:140769811-140769818 chr3:140769810-140769819
18	CTCF	chr3:140769940-140770090	HCPEpiC	choroid plexus:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
19	TCF12	chr3:140769605-140770304	ECC-1	luminal epithelium:	n/a	chr3:140769686-140769693 chr3:140770042-140770049
20	CTCF	chr3:140769920-140770070	GM12874	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
21	ZNF143	chr3:140769146-140770191	H1-hESC	embryonic stem cell:	n/a	chr3:140770067-140770077 chr3:140770014-140770024
22	TAF1	chr3:140769812-140770252	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr3:140769962-140770125	A549	lung:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
24	CTCF	chr3:140769840-140769990	HFF-Myc	foreskin:	n/a	n/a
25	CTCF	chr3:140769940-140770090	GM12865	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
26	ZNF263	chr3:140769364-140770792	HEK293-T-REx	kidney:	n/a	chr3:140769857-140769866
27	MAX	chr3:140769676-140770400	ECC-1	luminal epithelium:	n/a	chr3:140769762-140769772 chr3:140769811-140769818 chr3:140769810-140769819
28	EP300	chr3:140769936-140770354	ECC-1	luminal epithelium:	n/a	chr3:140770014-140770023 chr3:140770068-140770077 chr3:140770066-140770075
29	SIN3AK20	chr3:140769799-140770239	H1-hESC	embryonic stem cell:	n/a	n/a
30	ATF2	chr3:140769669-140770314	H1-hESC	embryonic stem cell:	n/a	n/a
31	CTCF	chr3:140769983-140770104	NHEK	skin:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
32	MAX	chr3:140769598-140770420	ECC-1	luminal epithelium:	n/a	chr3:140769762-140769772 chr3:140769811-140769818 chr3:140769810-140769819
33	CTCF	chr3:140769980-140770130	GM12875	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
34	CTCF	chr3:140769960-140770110	A549	lung:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
35	TCF12	chr3:140769715-140770500	ECC-1	luminal epithelium:	n/a	chr3:140770042-140770049
36	CTCF	chr3:140769960-140770110	GM12873	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
37	CTCF	chr3:140769980-140770130	HFF	foreskin:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
38	POLR2A	chr3:140769839-140770353	MCF-7	breast:	n/a	n/a
39	TAF1	chr3:140769773-140770285	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr3:140769978-140770104	Medullo	brain:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
41	RAD21	chr3:140769756-140770972	H1-hESC	embryonic stem cell:	n/a	chr3:140770060-140770072 chr3:140770036-140770055 chr3:140770040-140770054 chr3:140770536-140770546 chr3:140770334-140770344
42	CTCF	chr3:140769880-140770030	GM12875	blood:	n/a	n/a
43	YY1	chr3:140769882-140770153	SK-N-SH_RA	brain:	n/a	chr3:140770069-140770083 chr3:140769991-140770000 chr3:140770066-140770080 chr3:140770066-140770075 chr3:140769988-140769997 chr3:140770011-140770025 chr3:140770063-140770077
44	CEBPB	chr3:140769888-140770174	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr3:140769914-140770303	ECC-1	luminal epithelium:	n/a	chr3:140770060-140770072 chr3:140770036-140770055 chr3:140770040-140770054
46	ZBTB7A	chr3:140769809-140770315	ECC-1	luminal epithelium:	n/a	chr3:140770120-140770127
47	CHD1	chr3:140769682-140770094	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr3:140769940-140770090	GM12872	blood:	n/a	chr3:140770040-140770053 chr3:140770041-140770051 chr3:140770040-140770053 chr3:140770038-140770056
49	SIN3A	chr3:140769507-140771946	H1-hESC	embryonic stem cell:	n/a	chr3:140770847-140770856
50	MAX	chr3:140769707-140770300	A549	lung:	n/a	chr3:140769762-140769772 chr3:140769811-140769818 chr3:140769810-140769819

Variant related genes	Relation type
SPSB4	TF binding region

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432488	chr3:140752302-140790302	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv3342822	chr3:140769087-140772135	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv591889	chr3:140769896-140778138	Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140769000-140770000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:140769000-140770000	Flanking Active TSS	Dnd41	blood
3	chr3:140769200-140770000	Enhancers	Fetal Heart	heart
4	chr3:140769200-140770800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:140769400-140770000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
6	chr3:140769400-140770000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:140769400-140770000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:140769400-140770000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr3:140769400-140770000	Bivalent Enhancer	Lung	lung
10	chr3:140769400-140770000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr3:140769400-140770000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
12	chr3:140769400-140770600	Bivalent/Poised TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr3:140769400-140770600	Enhancers	Esophagus	oesophagus
14	chr3:140769400-140770800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:140769400-140770800	Enhancers	Liver	Liver
16	chr3:140769400-140771000	Bivalent/Poised TSS	NHEK	skin
17	chr3:140769400-140771200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr3:140769400-140771200	Active TSS	Fetal Brain Female	brain
19	chr3:140769400-140771400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
20	chr3:140769400-140771600	Bivalent Enhancer	Spleen	Spleen
21	chr3:140769400-140771800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:140769400-140772200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:140769400-140772400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:140769400-140772600	Active TSS	Fetal Kidney	kidney
25	chr3:140769600-140770000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:140769600-140770000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:140769600-140770000	Active TSS	Primary B cells from cord blood	blood
28	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
29	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
30	chr3:140769600-140770000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
33	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
36	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Placenta	Placenta
38	chr3:140769600-140770000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
39	chr3:140769600-140770000	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
40	chr3:140769600-140770000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr3:140769600-140770000	Bivalent Enhancer	HMEC	breast
42	chr3:140769600-140770200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:140769600-140770200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:140769600-140770200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:140769600-140770200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
46	chr3:140769600-140770400	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:140769600-140770400	Active TSS	Brain Germinal Matrix	brain
48	chr3:140769600-140770600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr3:140769600-140770600	Active TSS	Right Ventricle	heart
50	chr3:140769600-140770800	Active TSS	HSMM	muscle

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