Variant report

Variant	rs55774802
Chromosome Location	chr3:155462073-155462074
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	POLR2A	chr3:155461985-155462260	ProgFib	skin:	n/a	n/a
2	CTBP2	chr3:155461816-155463206	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP1	chr3:155461843-155463352	A549	lung:	n/a	chr3:155462884-155462895 chr3:155462885-155462899
4	POLR2A	chr3:155461795-155462288	HCT-116	colon:	n/a	n/a
5	MXI1	chr3:155461828-155462321	H1-hESC	embryonic stem cell:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
6	HMGN3	chr3:155461912-155463020	K562	blood:	n/a	n/a
7	E2F4	chr3:155462034-155462198	MCF10A-Er-Src	breast:	n/a	chr3:155462104-155462119
8	POLR2A	chr3:155461711-155463117	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr3:155461971-155462437	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:155461782-155463169	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3A	chr3:155461524-155463101	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:155461905-155462379	HepG2	liver:	n/a	n/a
13	BACH1	chr3:155462057-155463080	H1-hESC	embryonic stem cell:	n/a	n/a
14	REST	chr3:155461875-155462384	A549	lung:	n/a	chr3:155462231-155462244 chr3:155462011-155462024
15	POLR2A	chr3:155461879-155462299	A549	lung:	n/a	n/a
16	POLR2A	chr3:155461933-155462200	HepG2	liver:	n/a	n/a
17	CTCF	chr3:155461980-155462130	SK-N-SH_RA	brain:	n/a	n/a
18	POLR2A	chr3:155461880-155463078	MCF-7	breast:	n/a	n/a
19	TAF1	chr3:155461838-155463036	H1-neurons	neurons:	n/a	n/a
20	RCOR1	chr3:155461843-155462373	K562	blood:	n/a	n/a
21	HA-E2F1	chr3:155461710-155463204	MCF-7	breast:	n/a	chr3:155462003-155462012 chr3:155462857-155462866
22	NANOG	chr3:155461896-155462115	H1-hESC	embryonic stem cell:	n/a	n/a
23	NRF1	chr3:155461819-155462152	HepG2	liver:	n/a	chr3:155462002-155462016 chr3:155461999-155462013 chr3:155462001-155462012 chr3:155462002-155462011 chr3:155462002-155462013
24	NRF1	chr3:155461814-155462196	GM12878	blood:	n/a	chr3:155462002-155462016 chr3:155461999-155462013 chr3:155462001-155462012 chr3:155462002-155462011 chr3:155462002-155462013
25	MAX	chr3:155461795-155462571	A549	lung:	n/a	chr3:155461990-155461999
26	HEY1	chr3:155461817-155462265	HepG2	liver:	n/a	chr3:155462017-155462032
27	POLR2A	chr3:155461880-155462221	A549	lung:	n/a	n/a
28	YY1	chr3:155461923-155462443	A549	lung:	n/a	n/a
29	REST	chr3:155461339-155463168	H1-neurons	neurons:	n/a	chr3:155462231-155462244 chr3:155462011-155462024
30	MAX	chr3:155461818-155463098	ECC-1	luminal epithelium:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
31	POLR2A	chr3:155461857-155463020	Raji	blood:	n/a	n/a
32	MYC	chr3:155461949-155463142	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
33	POLR2A	chr3:155461908-155462230	H1-hESC	embryonic stem cell:	n/a	n/a
34	MAX	chr3:155461801-155463231	MCF-7	breast:	n/a	chr3:155461990-155461999 chr3:155462885-155462895
35	BRCA1	chr3:155461981-155462170	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr3:155461741-155463079	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr3:155461966-155462214	HepG2	liver:	n/a	n/a
38	YY1	chr3:155461970-155462239	HCT-116	colon:	n/a	n/a
39	POLR2A	chr3:155461874-155463135	HL-60	blood:	n/a	n/a
40	POLR2A	chr3:155461852-155462616	HepG2	liver:	n/a	n/a
41	SIN3AK20	chr3:155461816-155462155	HepG2	liver:	n/a	n/a
42	SPI1	chr3:155462015-155463180	HL-60	blood:	n/a	n/a
43	UBTF	chr3:155462038-155463004	K562	blood:	n/a	n/a
44	MXI1	chr3:155461328-155463302	SK-N-SH	brain:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
45	CCNT2	chr3:155461857-155462155	K562	blood:	n/a	chr3:155462028-155462037
46	POLR2A	chr3:155461883-155462275	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:155461853-155462256	HCT-116	colon:	n/a	n/a
48	NRF1	chr3:155461510-155462973	SK-N-SH	brain:	n/a	chr3:155462002-155462016 chr3:155461999-155462013 chr3:155462001-155462012 chr3:155462002-155462011 chr3:155462002-155462013
49	MXI1	chr3:155461965-155462143	K562	blood:	n/a	chr3:155461984-155461999 chr3:155461986-155462001
50	MAX	chr3:155461844-155463173	K562	blood:	n/a	chr3:155461990-155461999 chr3:155462885-155462895

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:155462063-155462113	GM12892	blood:	n/a
2	chr3:155462063-155462113	ECC-1	luminal epithelium:	n/a
3	chr3:155462063-155462113	MCF10A-Er-Src	breast:	n/a
4	chr3:155462063-155462113	CMK	blood:	n/a
5	chr3:155462063-155462113	BJ	skin:	n/a
6	chr3:155462063-155462113	AG10803	skin:	n/a
7	chr3:155462063-155462113	ovcar-3	ovarian:	n/a
8	chr3:155462063-155462113	ProgFib	skin:	n/a
9	chr3:155462063-155462113	HUVEC	blood vessel:	n/a
10	chr3:155462063-155462113	AG04449	skin:	fetal
11	chr3:155462063-155462113	K562	blood:	n/a
12	chr3:155462063-155462113	NT2-D1	testis:	n/a
13	chr3:155462063-155462113	AG09309	skin:	n/a
14	chr3:155462063-155462113	U87	brain:	n/a
15	chr3:155462063-155462113	LNCaP	prostate:	n/a
16	chr3:155462063-155462113	NB4	blood:	n/a
17	chr3:155462063-155462113	NH-A	brain:	n/a
18	chr3:155462063-155462113	GM12878	blood:	n/a
19	chr3:155462063-155462113	RPTEC	kidney:	n/a
20	chr3:155462063-155462113	Jurkat	blood:	n/a
21	chr3:155462063-155462113	Hela-S3	cervix:	n/a
22	chr3:155462063-155462113	PANC-1	pancreas:	n/a
23	chr3:155462063-155462113	SK-N-SH	brain:	n/a
24	chr3:155462063-155462113	HCPEpiC	choroid plexus:	n/a
25	chr3:155462063-155462113	SK-N-MC	brain:	n/a
26	chr3:155462063-155462113	HCF	heart:	n/a
27	chr3:155462063-155462113	NHDF-neo	bronchial:	n/a
28	chr3:155462063-155462113	HEEpiC	esophagus:	n/a
29	chr3:155462063-155462113	AG09319	gingival:	n/a
30	chr3:155462063-155462113	HCM	heart:	n/a
31	chr3:155462063-155462113	PFSK-1	brain:	n/a
32	chr3:155462063-155462113	AoSMC	blood vessel:	n/a
33	chr3:155462063-155462113	SK-N-SH_RA	brain:	n/a
34	chr3:155462063-155462113	T-47D	breast:	n/a
35	chr3:155462063-155462113	HPAEpiC	pulmonary alveolar:	n/a
36	chr3:155462063-155462113	GM12891	blood:	n/a
37	chr3:155462063-155462113	HEK293	kidney:	embryo
38	chr3:155462063-155462113	H1-hESC	embryonic stem cell:	embryo
39	chr3:155462063-155462113	Hepatocyte	liver:	n/a
40	chr3:155462063-155462113	MCF-7	breast:	n/a
41	chr3:155462063-155462113	BE2_C	brain:	n/a
42	chr3:155462063-155462113	HRE	kidney:	n/a
43	chr3:155462063-155462113	HNPCEpiC	eye:	n/a
44	chr3:155462063-155462113	IMR90	lung:	fetal
45	chr3:155462063-155462113	HRCEpiC	kidney:	n/a
46	chr3:155462063-155462113	SKMC	muscle:	n/a
47	chr3:155462063-155462113	HRPEpiC	eye:	n/a
48	chr3:155462063-155462113	HepG2	liver:	n/a
49	chr3:155462063-155462113	HIPEpiC	eye:	n/a
50	chr3:155462063-155462113	HAEpiC	amniotic membrane:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:155461486..155463918-chr3:155586998..155589713,4	K562	blood:
2	chr3:155461195..155464539-chr3:155588373..155590107,3	MCF-7	breast:
3	chr3:155460891..155464537-chr3:155570941..155574143,3	MCF-7	breast:
4	chr3:155462054..155464221-chr3:155571081..155573574,2	MCF-7	breast:
5	chr3:155461486..155465793-chr3:155586998..155592801,6	K562	blood:
6	chr3:155461523..155464397-chr3:155587900..155591398,5	MCF-7	breast:
7	chr3:155461931..155462531-chr8:43096224..43096734,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000214919	TF binding region
ENSG00000214919	CpG island
ENSG00000163655	Chromatin interaction
ENSG00000169359	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs56402298	0.92[AFR][1000 genomes]
rs60509211	1.00[AFR][1000 genomes]
rs61631059	0.92[AFR][1000 genomes]
rs73873406	0.92[AFR][1000 genomes]
rs73873408	1.00[AFR][1000 genomes]
rs73873413	1.00[AFR][1000 genomes]
rs73873417	1.00[AFR][1000 genomes]
rs73873419	0.92[AFR][1000 genomes]

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	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv829763	chr3:155417552-155470079	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155460800-155463600	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:155461000-155464400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:155461200-155462200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:155461200-155462800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:155461200-155463000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:155461200-155464200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:155461400-155462200	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:155461400-155462200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:155461400-155462200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:155461400-155462200	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr3:155461400-155462200	Bivalent/Poised TSS	GM12878-XiMat	blood
12	chr3:155461400-155462600	Active TSS	Fetal Kidney	kidney
13	chr3:155461400-155462800	Flanking Bivalent TSS/Enh	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:155461400-155462800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:155461400-155462800	Active TSS	Fetal Brain Male	brain
16	chr3:155461400-155462800	Active TSS	Hela-S3	cervix
17	chr3:155461400-155463000	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr3:155461400-155463000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:155461400-155463000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:155461400-155463000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
21	chr3:155461400-155463000	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr3:155461400-155463000	Flanking Bivalent TSS/Enh	Dnd41	blood
23	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
24	chr3:155461400-155463200	Active TSS	Left Ventricle	heart
25	chr3:155461400-155463200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr3:155461400-155463200	Bivalent/Poised TSS	HSMM	muscle
27	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:155461400-155463400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
29	chr3:155461400-155463600	Active TSS	Pancreas	Pancrea
30	chr3:155461400-155463800	Active TSS	Gastric	stomach
31	chr3:155461400-155463800	Active TSS	Right Ventricle	heart
32	chr3:155461400-155463800	Active TSS	A549	lung
33	chr3:155461400-155463800	Active TSS	NHLF	lung
34	chr3:155461400-155464000	Active TSS	H9 Cell Line	embryonic stem cell
35	chr3:155461400-155464000	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr3:155461400-155464000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:155461400-155464000	Active TSS	Right Atrium	heart
38	chr3:155461400-155464200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr3:155461400-155464200	Active TSS	Brain Angular Gyrus	brain
40	chr3:155461400-155464200	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:155461600-155462200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:155461600-155462200	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
43	chr3:155461600-155462200	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr3:155461600-155462400	Bivalent/Poised TSS	Fetal Brain Female	brain
45	chr3:155461600-155462400	Bivalent/Poised TSS	Stomach Mucosa	stomach
46	chr3:155461600-155462800	Active TSS	Stomach Smooth Muscle	stomach
47	chr3:155461600-155463000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:155461600-155463000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:155461600-155463000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:155461600-155463000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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