Variant report

Variant	rs553578993
Chromosome Location	chr12:32552020-32552021
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	chr12:32551963-32552238	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr12:32551849-32553556	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:32551981-32553421	MCF10A-Er-Src	breast:	n/a	n/a
4	MAX	chr12:32551922-32553094	A549	lung:	n/a	chr12:32552147-32552157
5	POLR2A	chr12:32551778-32553420	Hela-S3	cervix:	n/a	n/a
6	ZBTB7A	chr12:32551770-32553171	ECC-1	luminal epithelium:	n/a	n/a
7	NFIC	chr12:32551624-32553415	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr12:32552020-32552170	Caco-2	colon:	n/a	chr12:32552131-32552139
9	TCF12	chr12:32551771-32553090	A549	lung:	n/a	chr12:32552166-32552173 chr12:32552936-32552943 chr12:32552871-32552881
10	TCF7L2	chr12:32551952-32552241	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr12:32552018-32553517	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr12:32551978-32552178	HepG2	liver:	n/a	chr12:32552147-32552157
13	POLR2A	chr12:32552020-32553335	Hela-S3	cervix:	n/a	n/a
14	TCF12	chr12:32551550-32553633	ECC-1	luminal epithelium:	n/a	chr12:32552166-32552173 chr12:32552936-32552943 chr12:32552871-32552881
15	EGR1	chr12:32551873-32553307	ECC-1	luminal epithelium:	n/a	chr12:32552188-32552197 chr12:32552233-32552243
16	TCF7L2	chr12:32551948-32553066	HCT-116	colon:	n/a	n/a
17	SIN3AK20	chr12:32552020-32553071	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr12:32551992-32553091	HCT-116	colon:	n/a	n/a
19	ESR1	chr12:32551883-32552401	ECC-1	luminal epithelium:	n/a	n/a
20	MAX	chr12:32552015-32552711	A549	lung:	n/a	chr12:32552147-32552157
21	POLR2A	chr12:32551925-32552337	ECC-1	luminal epithelium:	n/a	n/a
22	CTBP2	chr12:32551946-32553418	H1-hESC	embryonic stem cell:	n/a	n/a
23	NR3C1	chr12:32551982-32552456	ECC-1	luminal epithelium:	n/a	chr12:32552116-32552129 chr12:32552297-32552313 chr12:32552298-32552312 chr12:32552298-32552313 chr12:32552298-32552312 chr12:32552297-32552313
24	EGR1	chr12:32551938-32552402	ECC-1	luminal epithelium:	n/a	chr12:32552188-32552197 chr12:32552233-32552243
25	CEBPB	chr12:32551931-32553167	ECC-1	luminal epithelium:	n/a	chr12:32552412-32552420
26	CREB1	chr12:32551959-32552863	A549	lung:	n/a	n/a
27	POLR2A	chr12:32551920-32552918	HUVEC	blood vessel:	n/a	n/a
28	SIN3A	chr12:32551710-32554057	H1-hESC	embryonic stem cell:	n/a	chr12:32552230-32552241 chr12:32552960-32552971 chr12:32552074-32552088 chr12:32552940-32552951
29	E2F1	chr12:32552013-32553074	Hela-S3	cervix:	n/a	chr12:32552412-32552421 chr12:32552269-32552284 chr12:32552238-32552248 chr12:32552225-32552240
30	POLR2A	chr12:32551954-32552214	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr12:32551959-32553181	A549	lung:	n/a	n/a
32	MAX	chr12:32551825-32553597	HCT-116	colon:	n/a	chr12:32552147-32552157
33	TAF1	chr12:32551759-32553487	ECC-1	luminal epithelium:	n/a	n/a
34	YY1	chr12:32551962-32553174	ECC-1	luminal epithelium:	n/a	chr12:32552274-32552288 chr12:32552230-32552241
35	ZEB1	chr12:32551829-32553352	HepG2	liver:	n/a	chr12:32552135-32552142 chr12:32552164-32552175
36	USF1	chr12:32551939-32552962	ECC-1	luminal epithelium:	n/a	chr12:32552178-32552194 chr12:32552448-32552464 chr12:32552132-32552148
37	SMARCC1	chr12:32551696-32553126	Hela-S3	cervix:	n/a	n/a
38	MAX	chr12:32552010-32552885	K562	blood:	n/a	chr12:32552147-32552157
39	TAF1	chr12:32551970-32553596	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr12:32551972-32553153	HepG2	liver:	n/a	chr12:32552147-32552157
41	POLR2A	chr12:32551890-32553176	ECC-1	luminal epithelium:	n/a	n/a
42	ZNF263	chr12:32551994-32553464	HEK293-T-REx	kidney:	n/a	n/a
43	MAZ	chr12:32551667-32553200	IMR90	lung:	n/a	chr12:32552147-32552157
44	HA-E2F1	chr12:32551758-32553350	MCF-7	breast:	n/a	chr12:32552412-32552421 chr12:32553185-32553194 chr12:32552269-32552284 chr12:32552238-32552248 chr12:32552225-32552240
45	HDAC2	chr12:32551807-32553203	MCF-7	breast:	n/a	chr12:32551967-32551976 chr12:32552189-32552198 chr12:32553158-32553172
46	MAX	chr12:32551683-32553559	ECC-1	luminal epithelium:	n/a	chr12:32552147-32552157
47	POLR2A	chr12:32551985-32553321	MCF-7	breast:	n/a	n/a
48	KAP1	chr12:32551766-32553358	HEK293	kidney:	n/a	n/a
49	TBP	chr12:32551901-32553706	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr12:32552014-32553919	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:32551988-32552038	PANC-1	pancreas:	n/a
2	chr12:32551988-32552038	ovcar-3	ovarian:	n/a
3	chr12:32551988-32552038	Hela-S3	cervix:	n/a
4	chr12:32551988-32552038	SKMC	muscle:	n/a
5	chr12:32551988-32552038	AG04450	lung:	fetal
6	chr12:32551988-32552038	H1-hESC	embryonic stem cell:	embryo
7	chr12:32551988-32552038	HRPEpiC	eye:	n/a
8	chr12:32551988-32552038	HAEpiC	amniotic membrane:	n/a
9	chr12:32551988-32552038	GM12892	blood:	n/a
10	chr12:32551988-32552038	AG09319	gingival:	n/a
11	chr12:32551988-32552038	NH-A	brain:	n/a
12	chr12:32551988-32552038	ProgFib	skin:	n/a
13	chr12:32551988-32552038	GM12878	blood:	n/a
14	chr12:32551988-32552038	HCF	heart:	n/a
15	chr12:32551988-32552038	CMK	blood:	n/a
16	chr12:32551988-32552038	AG10803	skin:	n/a
17	chr12:32551988-32552038	GM19239	blood:	n/a
18	chr12:32551988-32552038	HCM	heart:	n/a
19	chr12:32551988-32552038	NHBE	bronchial:	n/a
20	chr12:32551988-32552038	SK-N-MC	brain:	n/a
21	chr12:32551988-32552038	HepG2	liver:	n/a
22	chr12:32551988-32552038	Caco-2	colon:	n/a
23	chr12:32551988-32552038	PrEC	prostate:	n/a
24	chr12:32551988-32552038	NT2-D1	testis:	n/a
25	chr12:32551988-32552038	BJ	skin:	n/a
26	chr12:32551988-32552038	HL-60	blood:	n/a
27	chr12:32551988-32552038	MCF-7	breast:	n/a
28	chr12:32551988-32552038	IMR90	lung:	fetal
29	chr12:32551988-32552038	GM12891	blood:	n/a
30	chr12:32551988-32552038	RPTEC	kidney:	n/a
31	chr12:32551988-32552038	AoSMC	blood vessel:	n/a
32	chr12:32551988-32552038	HEK293	kidney:	embryo
33	chr12:32551988-32552038	AG04449	skin:	fetal
34	chr12:32551988-32552038	HEEpiC	esophagus:	n/a
35	chr12:32551988-32552038	Hepatocyte	liver:	n/a
36	chr12:32551988-32552038	ECC-1	luminal epithelium:	n/a
37	chr12:32551988-32552038	HCPEpiC	choroid plexus:	n/a
38	chr12:32551988-32552038	HMEC	breast:	n/a
39	chr12:32551988-32552038	SAEC	small airway:	n/a
40	chr12:32551988-32552038	AG09309	skin:	n/a
41	chr12:32551988-32552038	HCT-116	colon:	n/a
42	chr12:32551988-32552038	Jurkat	blood:	n/a
43	chr12:32551988-32552038	HRE	kidney:	n/a
44	chr12:32551988-32552038	NHDF-neo	bronchial:	n/a
45	chr12:32551988-32552038	T-47D	breast:	n/a
46	chr12:32551988-32552038	SK-N-SH	brain:	n/a
47	chr12:32551988-32552038	NB4	blood:	n/a
48	chr12:32551988-32552038	BE2_C	brain:	n/a
49	chr12:32551988-32552038	HNPCEpiC	eye:	n/a
50	chr12:32551988-32552038	PFSK-1	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:32550852..32553049-chr12:32831118..32832629,2	MCF-7	breast:
2	chr12:32551025..32552744-chr12:32831132..32833604,2	K562	blood:
3	chr12:32547740..32549812-chr12:32551795..32554175,2	MCF-7	breast:

Variant related genes	Relation type
FGD4	TF binding region
ENSG00000207176	TF binding region
ENSG00000207176	CpG island
FGD4	CpG island
ENSG00000087470	Chromatin interaction
ENSG00000207176	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv469346	chr12:32531220-32587465	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv558188	chr12:32531220-32587465	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
7	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3324783	chr12:32551310-32553858	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv3427823	chr12:32551585-32553583	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	8 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	chr12:32550800-32552200	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr12:32551200-32554800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:32551600-32552200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
4	chr12:32551600-32552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:32551600-32552200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32551600-32552200	Flanking Active TSS	Colonic Mucosa	Colon
7	chr12:32551600-32552200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:32551600-32552200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr12:32551600-32552200	Flanking Active TSS	Hela-S3	cervix
10	chr12:32551600-32552400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:32551600-32553000	Active TSS	Brain Angular Gyrus	brain
12	chr12:32551600-32553600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr12:32551600-32553800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr12:32551600-32553800	Active TSS	Rectal Smooth Muscle	rectum
15	chr12:32551600-32554200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:32551800-32552200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
20	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
21	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
22	chr12:32551800-32552200	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:32551800-32552200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr12:32551800-32552200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
26	chr12:32551800-32552200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:32551800-32552200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:32551800-32552200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr12:32551800-32552200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:32551800-32552200	Flanking Active TSS	Liver	Liver
32	chr12:32551800-32552200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:32551800-32552200	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr12:32551800-32552200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr12:32551800-32552200	Flanking Active TSS	Fetal Heart	heart
36	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
37	chr12:32551800-32552200	Flanking Active TSS	Placenta	Placenta
38	chr12:32551800-32552200	Flanking Active TSS	Pancreas	Pancrea
39	chr12:32551800-32552200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr12:32551800-32552200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:32551800-32552200	Flanking Bivalent TSS/Enh	Dnd41	blood
42	chr12:32551800-32552200	Flanking Active TSS	HMEC	breast
43	chr12:32551800-32552200	Flanking Active TSS	HUVEC	blood vessel
44	chr12:32551800-32552200	Flanking Active TSS	K562	blood
45	chr12:32551800-32552200	Flanking Active TSS	NH-A	brain
46	chr12:32551800-32552200	Flanking Active TSS	NHDF-Ad	bronchial
47	chr12:32551800-32552200	Flanking Active TSS	NHEK	skin
48	chr12:32551800-32552400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
49	chr12:32551800-32552400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
50	chr12:32551800-32552400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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