Variant report

Variant	rs527443908
Chromosome Location	chr3:142720338-142720339
allele	A/C
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	ZBTB33	chr3:142719803-142720727	SK-N-SH	brain:	n/a	n/a
2	FOSL2	chr3:142720139-142720572	A549	lung:	n/a	n/a
3	TAF1	chr3:142719817-142720660	GM12892	blood:	n/a	n/a
4	ATF3	chr3:142720082-142720499	H1-hESC	embryonic stem cell:	n/a	chr3:142720321-142720341 chr3:142720321-142720330
5	POLR2A	chr3:142719252-142721364	GM12878	blood:	n/a	n/a
6	NFATC1	chr3:142720072-142720706	GM12878	blood:	n/a	chr3:142720142-142720156
7	POLR2A	chr3:142719852-142721216	HepG2	liver:	n/a	n/a
8	EGR1	chr3:142720095-142720623	H1-hESC	embryonic stem cell:	n/a	n/a
9	NR2C2	chr3:142720160-142720608	K562	blood:	n/a	n/a
10	MAX	chr3:142719294-142721539	HepG2	liver:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
11	STAT5A	chr3:142719814-142720836	GM12878	blood:	n/a	n/a
12	THAP1	chr3:142720216-142720472	K562	blood:	n/a	n/a
13	BHLHE40	chr3:142719609-142720822	GM12878	blood:	n/a	chr3:142720319-142720332 chr3:142720321-142720330 chr3:142720320-142720329 chr3:142720321-142720330 chr3:142720322-142720331 chr3:142720433-142720449
14	ZNF143	chr3:142719871-142720641	GM12878	blood:	n/a	n/a
15	USF2	chr3:142720131-142720525	K562	blood:	n/a	chr3:142720319-142720332 chr3:142720321-142720330 chr3:142720320-142720329 chr3:142720319-142720330 chr3:142720321-142720330 chr3:142720322-142720331 chr3:142720433-142720449
16	REST	chr3:142719762-142721412	HL-60	blood:	n/a	chr3:142720854-142720874 chr3:142720854-142720874 chr3:142721035-142721048
17	JUND	chr3:142720040-142720613	H1-hESC	embryonic stem cell:	n/a	n/a
18	REST	chr3:142720219-142720591	H1-hESC	embryonic stem cell:	n/a	n/a
19	MXI1	chr3:142719220-142721923	Hela-S3	cervix:	n/a	chr3:142721094-142721103
20	CEBPB	chr3:142720217-142720564	A549	lung:	n/a	n/a
21	STAT5A	chr3:142719800-142720721	K562	blood:	n/a	n/a
22	USF2	chr3:142719294-142720570	Hela-S3	cervix:	n/a	chr3:142720319-142720332 chr3:142720321-142720330 chr3:142720320-142720329 chr3:142720319-142720330 chr3:142720321-142720330 chr3:142720322-142720331 chr3:142720433-142720449
23	MAX	chr3:142719766-142721541	ECC-1	luminal epithelium:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
24	SP1	chr3:142720097-142720665	GM12878	blood:	n/a	n/a
25	MAX	chr3:142720015-142720570	HepG2	liver:	n/a	chr3:142720319-142720327 chr3:142720321-142720330
26	POLR2A	chr3:142719768-142720854	ProgFib	skin:	n/a	n/a
27	MAX	chr3:142720124-142720541	K562	blood:	n/a	chr3:142720319-142720327 chr3:142720321-142720330
28	ZNF143	chr3:142720043-142720639	K562	blood:	n/a	n/a
29	CTCF	chr3:142720200-142720350	BE2_C	brain:	n/a	n/a
30	MAZ	chr3:142719874-142720878	Hela-S3	cervix:	n/a	chr3:142720319-142720327 chr3:142720321-142720330
31	ELF1	chr3:142719947-142720601	K562	blood:	n/a	chr3:142720310-142720323 chr3:142720312-142720323
32	MXI1	chr3:142719180-142721608	IMR90	lung:	n/a	chr3:142721094-142721103
33	RFX5	chr3:142720166-142720441	K562	blood:	n/a	n/a
34	REST	chr3:142720303-142720819	ECC-1	luminal epithelium:	n/a	n/a
35	TAF1	chr3:142719965-142720684	SK-N-SH	brain:	n/a	n/a
36	TAF1	chr3:142719820-142721037	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr3:142719742-142720864	GM12891	blood:	n/a	n/a
38	CEBPB	chr3:142720230-142720431	HepG2	liver:	n/a	n/a
39	WRNIP1	chr3:142719833-142721449	GM12878	blood:	n/a	n/a
40	POLR2A	chr3:142719864-142720891	A549	lung:	n/a	n/a
41	MBD4	chr3:142719821-142720724	HepG2	liver:	n/a	n/a
42	MXI1	chr3:142719929-142721536	H1-hESC	embryonic stem cell:	n/a	chr3:142721094-142721103
43	JUN	chr3:142719815-142720629	K562	blood:	n/a	chr3:142719831-142719843
44	CUX1	chr3:142719925-142720672	K562	blood:	n/a	n/a
45	USF1	chr3:142720025-142720536	SK-N-SH_RA	brain:	n/a	chr3:142720319-142720332 chr3:142720321-142720330 chr3:142720320-142720329 chr3:142720319-142720330 chr3:142720321-142720330 chr3:142720322-142720331 chr3:142720433-142720449
46	MYC	chr3:142719887-142721480	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
47	CHD1	chr3:142719781-142720764	GM12878	blood:	n/a	n/a
48	POU2F2	chr3:142720161-142720538	GM12878	blood:	n/a	n/a
49	REST	chr3:142719848-142720805	H1-neurons	neurons:	n/a	n/a
50	TCF12	chr3:142720044-142720737	A549	lung:	n/a	chr3:142720211-142720218

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142720294-142720344	Caco-2	colon:	n/a
2	chr3:142720292-142720342	CMK	blood:	n/a
3	chr3:142720292-142720342	ECC-1	luminal epithelium:	n/a
4	chr3:142720294-142720344	K562	blood:	n/a
5	chr3:142720294-142720344	HCM	heart:	n/a
6	chr3:142720292-142720342	GM19239	blood:	n/a
7	chr3:142720316-142720366	SAEC	small airway:	n/a
8	chr3:142720294-142720344	GM12891	blood:	n/a
9	chr3:142720316-142720366	HPAEpiC	pulmonary alveolar:	n/a
10	chr3:142720292-142720342	SAEC	small airway:	n/a
11	chr3:142720292-142720342	T-47D	breast:	n/a
12	chr3:142720292-142720342	AG04449	skin:	fetal
13	chr3:142720316-142720366	PFSK-1	brain:	n/a
14	chr3:142720292-142720342	BE2_C	brain:	n/a
15	chr3:142720316-142720366	Caco-2	colon:	n/a
16	chr3:142720316-142720366	HEK293	kidney:	embryo
17	chr3:142720294-142720344	PrEC	prostate:	n/a
18	chr3:142720316-142720366	AG04450	lung:	fetal
19	chr3:142720316-142720366	SKMC	muscle:	n/a
20	chr3:142720316-142720366	NT2-D1	testis:	n/a
21	chr3:142720294-142720344	SK-N-SH_RA	brain:	n/a
22	chr3:142720316-142720366	IMR90	lung:	fetal
23	chr3:142720316-142720366	AG10803	skin:	n/a
24	chr3:142720316-142720366	HUVEC	blood vessel:	n/a
25	chr3:142720292-142720342	SKMC	muscle:	n/a
26	chr3:142720292-142720342	ovcar-3	ovarian:	n/a
27	chr3:142720292-142720342	Jurkat	blood:	n/a
28	chr3:142720294-142720344	MCF10A-Er-Src	breast:	n/a
29	chr3:142720292-142720342	GM12891	blood:	n/a
30	chr3:142720316-142720366	HCF	heart:	n/a
31	chr3:142720294-142720344	HCF	heart:	n/a
32	chr3:142720316-142720366	PANC-1	pancreas:	n/a
33	chr3:142720316-142720366	HepG2	liver:	n/a
34	chr3:142720292-142720342	AG10803	skin:	n/a
35	chr3:142720316-142720366	Hepatocyte	liver:	n/a
36	chr3:142720294-142720344	T-47D	breast:	n/a
37	chr3:142720292-142720342	RPTEC	kidney:	n/a
38	chr3:142720292-142720342	GM12892	blood:	n/a
39	chr3:142720294-142720344	HNPCEpiC	eye:	n/a
40	chr3:142720294-142720344	CMK	blood:	n/a
41	chr3:142720292-142720342	Hepatocyte	liver:	n/a
42	chr3:142720292-142720342	HCT-116	colon:	n/a
43	chr3:142720294-142720344	ovcar-3	ovarian:	n/a
44	chr3:142720292-142720342	HEEpiC	esophagus:	n/a
45	chr3:142720294-142720344	NHDF-neo	bronchial:	n/a
46	chr3:142720294-142720344	AG09309	skin:	n/a
47	chr3:142720294-142720344	SK-N-MC	brain:	n/a
48	chr3:142720292-142720342	HPAEpiC	pulmonary alveolar:	n/a
49	chr3:142720294-142720344	AG09319	gingival:	n/a
50	chr3:142720316-142720366	HCM	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142296202..142300183-chr3:142719946..142722583,4	K562	blood:
2	chr3:142605846..142608751-chr3:142718093..142722238,5	K562	blood:
3	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
4	chr3:142718714..142720649-chr8:146127096..146128737,2	MCF-7	breast:
5	chr3:142717299..142720622-chr3:142733961..142737185,3	MCF-7	breast:
6	chr3:142677697..142680198-chr3:142718866..142721394,3	K562	blood:
7	chr3:142676730..142680278-chr3:142717890..142721546,3	K562	blood:
8	chr3:142442669..142444351-chr3:142720029..142722522,2	MCF-7	breast:
9	chr3:142718594..142721364-chr3:142729652..142733132,4	MCF-7	breast:
10	chr3:142719836..142721441-chr3:142742742..142745727,2	K562	blood:
11	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
12	chr3:142681877..142683958-chr3:142718843..142721049,2	K562	blood:
13	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-U2SURP-2	chr3:142719869-142720401	ENSG00000241570.4

Variant related genes	Relation type
ENSG00000268129	TF binding region
U2SURP	TF binding region
ENSG00000268129	CpG island
U2SURP	CpG island
ENSG00000175054	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000163710	Chromatin interaction
ENSG00000241592	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000196150	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000242390	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 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	chr3:142718200-142725000	Active TSS	K562	blood
2	chr3:142718400-142721800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:142718400-142722000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr3:142718400-142722400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:142718600-142722200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:142718600-142722200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:142718800-142720600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:142718800-142721800	Active TSS	Left Ventricle	heart
9	chr3:142718800-142722200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:142718800-142722400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr3:142718800-142722400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:142718800-142722400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:142718800-142723000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:142719000-142721400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:142719000-142721800	Active TSS	Right Atrium	heart
16	chr3:142719000-142722000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr3:142719000-142722200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:142719000-142722200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:142719000-142722200	Active TSS	HSMMtube	muscle
20	chr3:142719000-142722800	Active TSS	A549	lung
21	chr3:142719200-142721600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr3:142719200-142721800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr3:142719200-142721800	Active TSS	Ovary	ovary
24	chr3:142719200-142722000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:142719200-142722000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:142719200-142722200	Active TSS	NHLF	lung
27	chr3:142719200-142723400	Active TSS	GM12878-XiMat	blood
28	chr3:142719400-142720400	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr3:142719400-142721400	Active TSS	Fetal Heart	heart
30	chr3:142719400-142721600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:142719400-142721600	Active TSS	Gastric	stomach
32	chr3:142719400-142721600	Active TSS	Lung	lung
33	chr3:142719400-142721800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:142719400-142721800	Active TSS	Esophagus	oesophagus
35	chr3:142719400-142722000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr3:142719400-142722000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:142719400-142722000	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:142719400-142722000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:142719400-142722000	Active TSS	Fetal Intestine Large	intestine
40	chr3:142719400-142722200	Active TSS	Hela-S3	cervix
41	chr3:142719400-142722200	Active TSS	NHDF-Ad	bronchial
42	chr3:142719400-142722400	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr3:142719400-142722400	Active TSS	NHEK	skin
44	chr3:142719600-142721000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:142719600-142721000	Active TSS	Fetal Brain Female	brain
46	chr3:142719600-142721000	Active TSS	Stomach Smooth Muscle	stomach
47	chr3:142719600-142721200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:142719600-142721200	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:142719600-142721200	Active TSS	Brain Substantia Nigra	brain
50	chr3:142719600-142721200	Active TSS	Duodenum Mucosa	Duodenum

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