Variant report

Variant	rs140851741
Chromosome Location	chr3:142682388-142682389
allele	G/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	chr3:142682374-142683209	HepG2	liver:	n/a	n/a
2	JUND	chr3:142682283-142682886	A549	lung:	n/a	n/a
3	MAX	chr3:142682257-142682976	K562	blood:	n/a	chr3:142682825-142682834
4	CCNT2	chr3:142682282-142683220	K562	blood:	n/a	n/a
5	YY1	chr3:142682334-142682856	K562	blood:	n/a	chr3:142682537-142682551 chr3:142682773-142682787 chr3:142682770-142682779 chr3:142682542-142682553 chr3:142682543-142682557 chr3:142682548-142682557 chr3:142682745-142682759 chr3:142682709-142682723 chr3:142682539-142682550 chr3:142682542-142682551 chr3:142682715-142682729 chr3:142682545-142682554
6	E2F6	chr3:142682319-142682903	A549	lung:	n/a	chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
7	TAF1	chr3:142682267-142682840	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:142682321-142682551	ECC-1	luminal epithelium:	n/a	n/a
9	TBP	chr3:142682342-142682877	K562	blood:	n/a	n/a
10	REST	chr3:142681914-142683570	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr3:142681583-142683285	PBDE	blood:	n/a	n/a
12	POLR2A	chr3:142682366-142682660	A549	lung:	n/a	n/a
13	MAX	chr3:142682234-142683436	H1-hESC	embryonic stem cell:	n/a	chr3:142682825-142682834
14	HEY1	chr3:142682297-142682916	HepG2	liver:	n/a	chr3:142682541-142682556 chr3:142682538-142682553 chr3:142682544-142682559
15	MAX	chr3:142682384-142682914	K562	blood:	n/a	chr3:142682825-142682834
16	YY1	chr3:142682304-142682690	K562	blood:	n/a	chr3:142682537-142682551 chr3:142682542-142682553 chr3:142682543-142682557 chr3:142682548-142682557 chr3:142682539-142682550 chr3:142682542-142682551 chr3:142682545-142682554
17	HEY1	chr3:142682152-142682921	HepG2	liver:	n/a	chr3:142682541-142682556 chr3:142682538-142682553 chr3:142682544-142682559
18	POLR2A	chr3:142682296-142682881	K562	blood:	n/a	n/a
19	TAF1	chr3:142681826-142682870	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr3:142682206-142683317	H1-hESC	embryonic stem cell:	n/a	chr3:142682825-142682834
21	HMGN3	chr3:142681685-142683281	K562	blood:	n/a	n/a
22	POLR2A	chr3:142682329-142682908	A549	lung:	n/a	n/a
23	MAX	chr3:142682117-142683289	HepG2	liver:	n/a	chr3:142682825-142682834
24	POLR2A	chr3:142682346-142682941	A549	lung:	n/a	n/a
25	CTCF	chr3:142682260-142682410	SK-N-SH_RA	brain:	n/a	n/a
26	HEY1	chr3:142682310-142682884	K562	blood:	n/a	chr3:142682541-142682556 chr3:142682538-142682553 chr3:142682544-142682559
27	EP300	chr3:142682229-142682897	ECC-1	luminal epithelium:	n/a	chr3:142682543-142682552 chr3:142682745-142682754 chr3:142682543-142682559 chr3:142682548-142682557
28	YY1	chr3:142681850-142682987	HepG2	liver:	n/a	chr3:142682537-142682551 chr3:142682773-142682787 chr3:142682770-142682779 chr3:142682542-142682553 chr3:142682543-142682557 chr3:142682548-142682557 chr3:142682745-142682759 chr3:142682709-142682723 chr3:142682539-142682550 chr3:142682542-142682551 chr3:142682715-142682729 chr3:142682545-142682554
29	E2F6	chr3:142682298-142683261	K562	blood:	n/a	chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
30	TAF1	chr3:142682375-142682769	HepG2	liver:	n/a	n/a
31	POLR2A	chr3:142682303-142683540	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:142682244-142682869	HepG2	liver:	n/a	n/a
33	ARID3A	chr3:142682173-142682756	HepG2	liver:	n/a	n/a
34	TAF1	chr3:142682387-142682775	HepG2	liver:	n/a	n/a
35	E2F6	chr3:142681102-142682892	H1-hESC	embryonic stem cell:	n/a	chr3:142682194-142682208 chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
36	ZBTB7A	chr3:142682182-142683057	K562	blood:	n/a	n/a
37	MAX	chr3:142681257-142683103	A549	lung:	n/a	chr3:142682825-142682834
38	UBTF	chr3:142682340-142683052	K562	blood:	n/a	n/a
39	E2F6	chr3:142682328-142682917	K562	blood:	n/a	chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
40	CTCF	chr3:142682240-142682390	SK-N-SH_RA	brain:	n/a	n/a
41	POLR2A	chr3:142681737-142683308	H1-hESC	embryonic stem cell:	n/a	n/a
42	E2F6	chr3:142682271-142682899	K562	blood:	n/a	chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
43	POLR2A	chr3:142682328-142682741	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr3:142682374-142682907	K562	blood:	n/a	chr3:142682825-142682834
45	E2F4	chr3:142682312-142683324	K562	blood:	n/a	chr3:142682642-142682651 chr3:142682543-142682553 chr3:142682546-142682556 chr3:142682773-142682782
46	EGR1	chr3:142682167-142682931	K562	blood:	n/a	chr3:142682777-142682786 chr3:142682179-142682189
47	MAX	chr3:142682016-142683054	A549	lung:	n/a	chr3:142682825-142682834
48	POLR2A	chr3:142682218-142682881	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:142682371-142682716	A549	lung:	n/a	n/a
50	POLR2A	chr3:142682258-142682958	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142682378-142682428	IMR90	lung:	fetal
2	chr3:142682378-142682428	HCT-116	colon:	n/a
3	chr3:142682378-142682428	PFSK-1	brain:	n/a
4	chr3:142682378-142682428	AG09319	gingival:	n/a
5	chr3:142682378-142682428	LNCaP	prostate:	n/a
6	chr3:142682378-142682428	HEK293	kidney:	embryo
7	chr3:142682378-142682428	AG04450	lung:	fetal
8	chr3:142682378-142682428	PANC-1	pancreas:	n/a
9	chr3:142682378-142682428	Caco-2	colon:	n/a
10	chr3:142682378-142682428	HIPEpiC	eye:	n/a
11	chr3:142682378-142682428	CMK	blood:	n/a
12	chr3:142682378-142682428	GM12878	blood:	n/a
13	chr3:142682378-142682428	H1-hESC	embryonic stem cell:	embryo
14	chr3:142682378-142682428	GM06990	blood:	n/a
15	chr3:142682378-142682428	MCF10A-Er-Src	breast:	n/a
16	chr3:142682378-142682428	K562	blood:	n/a
17	chr3:142682378-142682428	HCPEpiC	choroid plexus:	n/a
18	chr3:142682378-142682428	HUVEC	blood vessel:	n/a
19	chr3:142682378-142682428	ProgFib	skin:	n/a
20	chr3:142682378-142682428	RPTEC	kidney:	n/a
21	chr3:142682378-142682428	T-47D	breast:	n/a
22	chr3:142682378-142682428	Hela-S3	cervix:	n/a
23	chr3:142682378-142682428	SK-N-SH	brain:	n/a
24	chr3:142682378-142682428	GM19239	blood:	n/a
25	chr3:142682378-142682428	ovcar-3	ovarian:	n/a
26	chr3:142682378-142682428	HepG2	liver:	n/a
27	chr3:142682378-142682428	HL-60	blood:	n/a
28	chr3:142682378-142682428	HEEpiC	esophagus:	n/a
29	chr3:142682378-142682428	AG04449	skin:	fetal
30	chr3:142682378-142682428	HRE	kidney:	n/a
31	chr3:142682378-142682428	SAEC	small airway:	n/a
32	chr3:142682378-142682428	GM12891	blood:	n/a
33	chr3:142682378-142682428	SK-N-MC	brain:	n/a
34	chr3:142682378-142682428	NHDF-neo	bronchial:	n/a
35	chr3:142682378-142682428	HMEC	breast:	n/a
36	chr3:142682378-142682428	BE2_C	brain:	n/a
37	chr3:142682378-142682428	Jurkat	blood:	n/a
38	chr3:142682378-142682428	SKMC	muscle:	n/a
39	chr3:142682378-142682428	HRCEpiC	kidney:	n/a
40	chr3:142682378-142682428	HAEpiC	amniotic membrane:	n/a
41	chr3:142682378-142682428	NHBE	bronchial:	n/a
42	chr3:142682378-142682428	HNPCEpiC	eye:	n/a
43	chr3:142682378-142682428	NB4	blood:	n/a
44	chr3:142682378-142682428	HCM	heart:	n/a
45	chr3:142682378-142682428	NT2-D1	testis:	n/a
46	chr3:142682378-142682428	HRPEpiC	eye:	n/a
47	chr3:142682378-142682428	PrEC	prostate:	n/a
48	chr3:142682378-142682428	AG10803	skin:	n/a
49	chr3:142682378-142682428	BJ	skin:	n/a
50	chr3:142682378-142682428	HPAEpiC	pulmonary alveolar:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142681877..142683958-chr3:142718843..142721049,2	K562	blood:
2	chr3:142296891..142299259-chr3:142680803..142682548,2	K562	blood:

Variant related genes	Relation type
U2SURP	TF binding region
PAQR9	TF binding region
ENSG00000241570	TF binding region
U2SURP	CpG island
PAQR9	CpG island
ENSG00000241570	CpG island
ENSG00000268129	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000163714	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	esv3443662	chr3:142681287-142684135	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
4	esv3388028	chr3:142681537-142683935	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142681000-142683600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:142681400-142683400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr3:142681400-142683400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr3:142681400-142683600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:142681400-142683600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:142681400-142683600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:142681600-142682400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:142681600-142682600	Bivalent Enhancer	Placenta	Placenta
9	chr3:142681600-142683000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr3:142681600-142683000	Active TSS	Psoas Muscle	Psoas
11	chr3:142681600-142683200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
12	chr3:142681600-142683400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:142681600-142683400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
14	chr3:142681600-142683400	Bivalent/Poised TSS	NHEK	skin
15	chr3:142681600-142683600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr3:142681600-142683600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:142681600-142683800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
18	chr3:142681800-142682400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr3:142681800-142682400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:142681800-142682400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:142681800-142682600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
22	chr3:142681800-142682800	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr3:142681800-142682800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:142681800-142683000	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:142681800-142683000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
26	chr3:142681800-142683000	Bivalent/Poised TSS	HSMM	muscle
27	chr3:142681800-142683000	Bivalent/Poised TSS	HUVEC	blood vessel
28	chr3:142681800-142683200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:142681800-142683200	Active TSS	Fetal Brain Female	brain
30	chr3:142681800-142683400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:142681800-142683400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:142681800-142683400	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
33	chr3:142681800-142683400	Active TSS	Brain Angular Gyrus	brain
34	chr3:142681800-142683400	Bivalent/Poised TSS	Fetal Kidney	kidney
35	chr3:142681800-142683400	Active TSS	Left Ventricle	heart
36	chr3:142681800-142683400	Bivalent/Poised TSS	NHLF	lung
37	chr3:142681800-142683800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:142682000-142682400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr3:142682000-142682400	Enhancers	Pancreas	Pancrea
40	chr3:142682000-142682600	Bivalent/Poised TSS	Primary T helper cells fromperipheralblood	blood
41	chr3:142682000-142682800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:142682000-142682800	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr3:142682000-142682800	Bivalent/Poised TSS	Ovary	ovary
44	chr3:142682000-142683000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:142682000-142683000	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:142682000-142683000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:142682000-142683000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:142682000-142683000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr3:142682000-142683000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:142682000-142683000	Active TSS	Cortex derived primary cultured neurospheres	brain

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