Variant report

Variant	rs140095013
Chromosome Location	chr3:142720558-142720559
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	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	POLR2A	chr3:142719252-142721364	GM12878	blood:	n/a	n/a
5	NFATC1	chr3:142720072-142720706	GM12878	blood:	n/a	chr3:142720142-142720156
6	POLR2A	chr3:142719852-142721216	HepG2	liver:	n/a	n/a
7	EGR1	chr3:142720095-142720623	H1-hESC	embryonic stem cell:	n/a	n/a
8	NR2C2	chr3:142720160-142720608	K562	blood:	n/a	n/a
9	MAX	chr3:142719294-142721539	HepG2	liver:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
10	STAT5A	chr3:142719814-142720836	GM12878	blood:	n/a	n/a
11	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
12	ZNF143	chr3:142719871-142720641	GM12878	blood:	n/a	n/a
13	REST	chr3:142719762-142721412	HL-60	blood:	n/a	chr3:142720854-142720874 chr3:142720854-142720874 chr3:142721035-142721048
14	JUND	chr3:142720040-142720613	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr3:142720219-142720591	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr3:142719220-142721923	Hela-S3	cervix:	n/a	chr3:142721094-142721103
17	CEBPB	chr3:142720217-142720564	A549	lung:	n/a	n/a
18	STAT5A	chr3:142719800-142720721	K562	blood:	n/a	n/a
19	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
20	MAX	chr3:142719766-142721541	ECC-1	luminal epithelium:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
21	SP1	chr3:142720097-142720665	GM12878	blood:	n/a	n/a
22	MAX	chr3:142720015-142720570	HepG2	liver:	n/a	chr3:142720319-142720327 chr3:142720321-142720330
23	POLR2A	chr3:142719768-142720854	ProgFib	skin:	n/a	n/a
24	ZNF143	chr3:142720043-142720639	K562	blood:	n/a	n/a
25	MAZ	chr3:142719874-142720878	Hela-S3	cervix:	n/a	chr3:142720319-142720327 chr3:142720321-142720330
26	ELF1	chr3:142719947-142720601	K562	blood:	n/a	chr3:142720310-142720323 chr3:142720312-142720323
27	MXI1	chr3:142719180-142721608	IMR90	lung:	n/a	chr3:142721094-142721103
28	REST	chr3:142720303-142720819	ECC-1	luminal epithelium:	n/a	n/a
29	TAF1	chr3:142719965-142720684	SK-N-SH	brain:	n/a	n/a
30	TAF1	chr3:142719820-142721037	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr3:142719742-142720864	GM12891	blood:	n/a	n/a
32	WRNIP1	chr3:142719833-142721449	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:142719864-142720891	A549	lung:	n/a	n/a
34	MBD4	chr3:142719821-142720724	HepG2	liver:	n/a	n/a
35	MXI1	chr3:142719929-142721536	H1-hESC	embryonic stem cell:	n/a	chr3:142721094-142721103
36	JUN	chr3:142719815-142720629	K562	blood:	n/a	chr3:142719831-142719843
37	CUX1	chr3:142719925-142720672	K562	blood:	n/a	n/a
38	MYC	chr3:142719887-142721480	K562	blood:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
39	CHD1	chr3:142719781-142720764	GM12878	blood:	n/a	n/a
40	REST	chr3:142719848-142720805	H1-neurons	neurons:	n/a	n/a
41	TCF12	chr3:142720044-142720737	A549	lung:	n/a	chr3:142720211-142720218
42	MAX	chr3:142719674-142721739	A549	lung:	n/a	chr3:142721094-142721103 chr3:142720319-142720327 chr3:142721422-142721431 chr3:142720321-142720330
43	EP300	chr3:142719873-142720837	A549	lung:	n/a	chr3:142720641-142720650 chr3:142720315-142720322 chr3:142720441-142720450
44	ETS1	chr3:142720204-142720683	K562	blood:	n/a	chr3:142720315-142720325 chr3:142720314-142720323 chr3:142720314-142720323 chr3:142720310-142720326 chr3:142720314-142720323 chr3:142720311-142720324 chr3:142720314-142720323 chr3:142720314-142720323 chr3:142720314-142720323 chr3:142720314-142720323
45	YY1	chr3:142720259-142721442	K562	blood:	n/a	chr3:142721317-142721339 chr3:142720435-142720449 chr3:142720640-142720649 chr3:142720635-142720649 chr3:142721320-142721328
46	SMC3	chr3:142719940-142721116	Hela-S3	cervix:	n/a	n/a
47	POU2F2	chr3:142719810-142720727	GM12891	blood:	n/a	n/a
48	USF1	chr3:142719839-142720679	A549	lung:	n/a	chr3:142720319-142720332 chr3:142720321-142720330 chr3:142720320-142720329 chr3:142720319-142720330 chr3:142720321-142720330 chr3:142720322-142720331 chr3:142720433-142720449
49	GABPA	chr3:142719796-142720773	SK-N-SH	brain:	n/a	n/a
50	TEAD4	chr3:142719938-142720813	SK-N-SH	brain:	n/a	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	chr3:142295888..142299099-chr3:142720440..142723490,3	K562	blood:
4	chr3:142442417..142444804-chr3:142718685..142721847,4	K562	blood:
5	chr3:142718714..142720649-chr8:146127096..146128737,2	MCF-7	breast:
6	chr3:142717299..142720622-chr3:142733961..142737185,3	MCF-7	breast:
7	chr3:142677697..142680198-chr3:142718866..142721394,3	K562	blood:
8	chr3:142676730..142680278-chr3:142717890..142721546,3	K562	blood:
9	chr3:142442669..142444351-chr3:142720029..142722522,2	MCF-7	breast:
10	chr3:142718594..142721364-chr3:142729652..142733132,4	MCF-7	breast:
11	chr3:142719836..142721441-chr3:142742742..142745727,2	K562	blood:
12	chr3:142297403..142299294-chr3:142720282..142722143,3	MCF-7	breast:
13	chr3:142681877..142683958-chr3:142718843..142721049,2	K562	blood:
14	chr3:142295918..142298932-chr3:142719049..142722504,4	MCF-7	breast:

Variant related genes	Relation type
U2SURP	TF binding region
ENSG00000268129	TF binding region
ENSG00000163710	Chromatin interaction
ENSG00000188582	Chromatin interaction
ENSG00000144935	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000242390	Chromatin interaction
ENSG00000241592	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000196150	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	chr3:142719400-142721400	Active TSS	Fetal Heart	heart
29	chr3:142719400-142721600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:142719400-142721600	Active TSS	Gastric	stomach
31	chr3:142719400-142721600	Active TSS	Lung	lung
32	chr3:142719400-142721800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:142719400-142721800	Active TSS	Esophagus	oesophagus
34	chr3:142719400-142722000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:142719400-142722000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:142719400-142722000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr3:142719400-142722000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:142719400-142722000	Active TSS	Fetal Intestine Large	intestine
39	chr3:142719400-142722200	Active TSS	Hela-S3	cervix
40	chr3:142719400-142722200	Active TSS	NHDF-Ad	bronchial
41	chr3:142719400-142722400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr3:142719400-142722400	Active TSS	NHEK	skin
43	chr3:142719600-142721000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:142719600-142721000	Active TSS	Fetal Brain Female	brain
45	chr3:142719600-142721000	Active TSS	Stomach Smooth Muscle	stomach
46	chr3:142719600-142721200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:142719600-142721200	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr3:142719600-142721200	Active TSS	Brain Substantia Nigra	brain
49	chr3:142719600-142721200	Active TSS	Duodenum Mucosa	Duodenum
50	chr3:142719600-142721200	Active TSS	Rectal Smooth Muscle	rectum

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