Variant report

Variant	rs142479140
Chromosome Location	chr3:142840139-142840140
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:115)
CpG islands
(count:61)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:115 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:142839733-142840377	GM12878	blood:	n/a	n/a
2	MAX	chr3:142839617-142840158	K562	blood:	n/a	n/a
3	MYC	chr3:142839896-142840263	K562	blood:	n/a	n/a
4	BCLAF1	chr3:142839701-142840519	GM12878	blood:	n/a	n/a
5	CTCF	chr3:142839800-142840484	GM10266	blood:	n/a	n/a
6	POLR2A	chr3:142837773-142841232	GM19193	blood:	n/a	n/a
7	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
8	RAD21	chr3:142840131-142840680	A549	lung:	n/a	n/a
9	RAD21	chr3:142839731-142840584	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:142839609-142840422	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:142837371-142841744	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
13	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
14	RAD21	chr3:142840123-142840548	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr3:142837796-142841213	GM12878	blood:	n/a	n/a
16	RCOR1	chr3:142839827-142840418	GM12878	blood:	n/a	n/a
17	CTCF	chr3:142840125-142840535	H1-hESC	embryonic stem cell:	n/a	n/a
18	CHD2	chr3:142840064-142840423	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr3:142837372-142842950	GM12891	blood:	n/a	n/a
20	USF2	chr3:142839996-142840307	GM12878	blood:	n/a	n/a
21	CTCF	chr3:142840107-142840685	HCT-116	colon:	n/a	n/a
22	CTCF	chr3:142839787-142840536	K562	blood:	n/a	n/a
23	CTCF	chr3:142839760-142840566	IMR90	lung:	n/a	n/a
24	CTCF	chr3:142839696-142840741	GM12878	blood:	n/a	n/a
25	STAT5A	chr3:142839937-142840202	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:142837824-142840822	GM12878	blood:	n/a	n/a
27	E2F6	chr3:142838899-142840803	H1-hESC	embryonic stem cell:	n/a	chr3:142838914-142838924 chr3:142838911-142838921 chr3:142839536-142839546 chr3:142839574-142839584 chr3:142839630-142839639 chr3:142839543-142839552 chr3:142838917-142838927
28	CHD2	chr3:142839790-142840529	GM12878	blood:	n/a	n/a
29	CTCF	chr3:142840071-142840548	A549	lung:	n/a	n/a
30	MAX	chr3:142839884-142840531	A549	lung:	n/a	n/a
31	SIN3A	chr3:142837580-142840494	H1-hESC	embryonic stem cell:	n/a	chr3:142839059-142839070 chr3:142839574-142839587 chr3:142839203-142839214 chr3:142838852-142838863 chr3:142839021-142839030
32	POLR2A	chr3:142837371-142840452	GM12892	blood:	n/a	n/a
33	POLR2A	chr3:142839825-142840623	GM12878	blood:	n/a	n/a
34	ELF1	chr3:142839870-142840216	K562	blood:	n/a	n/a
35	MAX	chr3:142839714-142840627	GM12878	blood:	n/a	n/a
36	MAX	chr3:142839135-142840430	K562	blood:	n/a	n/a
37	USF2	chr3:142840010-142840644	H1-hESC	embryonic stem cell:	n/a	n/a
38	MAZ	chr3:142839804-142840462	GM12878	blood:	n/a	n/a
39	RAD21	chr3:142839762-142840614	H1-hESC	embryonic stem cell:	n/a	n/a
40	HMGN3	chr3:142837835-142840246	K562	blood:	n/a	n/a
41	CTCF	chr3:142840093-142840541	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr3:142839652-142840711	SK-N-SH	brain:	n/a	n/a
43	YY1	chr3:142839038-142840483	GM12892	blood:	n/a	chr3:142839630-142839639 chr3:142839364-142839378 chr3:142839628-142839642
44	EBF1	chr3:142840138-142840443	GM12878	blood:	n/a	n/a
45	RUNX3	chr3:142837697-142840604	GM12878	blood:	n/a	n/a
46	PAX5	chr3:142840067-142840555	GM12878	blood:	n/a	n/a
47	CTCF	chr3:142839743-142840569	GM12892	blood:	n/a	n/a
48	UBTF	chr3:142837118-142840212	K562	blood:	n/a	n/a
49	ZNF143	chr3:142839847-142840623	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr3:142839539-142840864	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142840129-142840179	HCM	heart:	n/a
2	chr3:142840129-142840179	HAEpiC	amniotic membrane:	n/a
3	chr3:142840129-142840179	AG04450	lung:	fetal
4	chr3:142840129-142840179	SK-N-SH_RA	brain:	n/a
5	chr3:142840129-142840179	ECC-1	luminal epithelium:	n/a
6	chr3:142840129-142840179	HPAEpiC	pulmonary alveolar:	n/a
7	chr3:142840129-142840179	RPTEC	kidney:	n/a
8	chr3:142840129-142840179	SAEC	small airway:	n/a
9	chr3:142840129-142840179	Hepatocyte	liver:	n/a
10	chr3:142840129-142840179	PFSK-1	brain:	n/a
11	chr3:142840129-142840179	HNPCEpiC	eye:	n/a
12	chr3:142840129-142840179	CMK	blood:	n/a
13	chr3:142840129-142840179	IMR90	lung:	fetal
14	chr3:142840129-142840179	SK-N-MC	brain:	n/a
15	chr3:142840129-142840179	BJ	skin:	n/a
16	chr3:142840129-142840179	A549	lung:	n/a
17	chr3:142840129-142840179	SK-N-SH	brain:	n/a
18	chr3:142840129-142840179	HL-60	blood:	n/a
19	chr3:142840129-142840179	HCT-116	colon:	n/a
20	chr3:142840129-142840179	AG09319	gingival:	n/a
21	chr3:142840129-142840179	PrEC	prostate:	n/a
22	chr3:142840129-142840179	GM12878	blood:	n/a
23	chr3:142840129-142840179	HepG2	liver:	n/a
24	chr3:142840129-142840179	Hela-S3	cervix:	n/a
25	chr3:142840129-142840179	NHBE	bronchial:	n/a
26	chr3:142840129-142840179	T-47D	breast:	n/a
27	chr3:142840129-142840179	NH-A	brain:	n/a
28	chr3:142840129-142840179	GM19239	blood:	n/a
29	chr3:142840129-142840179	HRE	kidney:	n/a
30	chr3:142840129-142840179	HCF	heart:	n/a
31	chr3:142840129-142840179	MCF10A-Er-Src	breast:	n/a
32	chr3:142840129-142840179	AG09309	skin:	n/a
33	chr3:142840129-142840179	HRCEpiC	kidney:	n/a
34	chr3:142840129-142840179	HUVEC	blood vessel:	n/a
35	chr3:142840129-142840179	Caco-2	colon:	n/a
36	chr3:142840129-142840179	ovcar-3	ovarian:	n/a
37	chr3:142840129-142840179	AG04449	skin:	fetal
38	chr3:142840129-142840179	GM06990	blood:	n/a
39	chr3:142840129-142840179	PANC-1	pancreas:	n/a
40	chr3:142840129-142840179	HEEpiC	esophagus:	n/a
41	chr3:142840129-142840179	SKMC	muscle:	n/a
42	chr3:142840129-142840179	AoSMC	blood vessel:	n/a
43	chr3:142840129-142840179	H1-hESC	embryonic stem cell:	embryo
44	chr3:142840129-142840179	NT2-D1	testis:	n/a
45	chr3:142840129-142840179	LNCaP	prostate:	n/a
46	chr3:142840129-142840179	K562	blood:	n/a
47	chr3:142840129-142840179	BE2_C	brain:	n/a
48	chr3:142840129-142840179	NHDF-neo	bronchial:	n/a
49	chr3:142840129-142840179	U87	brain:	n/a
50	chr3:142840129-142840179	ProgFib	skin:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142839497..142841574-chr3:143081300..143083347,2	K562	blood:
2	chr3:142777135..142778996-chr3:142838578..142841035,2	K562	blood:
3	chr3:142729466..142731298-chr3:142840071..142842956,2	K562	blood:
4	chr3:142795942..142798929-chr3:142838470..142841083,3	K562	blood:
5	chr3:142839097..142841882-chr3:143060810..143062990,2	K562	blood:
6	chr3:142546469..142548561-chr3:142838535..142840408,2	K562	blood:
7	chr3:142719801..142721977-chr3:142838395..142840175,2	K562	blood:
8	chr3:142729466..142732055-chr3:142838748..142841571,2	K562	blood:
9	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
10	chr3:142839303..142841374-chr3:143036089..143037614,2	K562	blood:
11	chr3:142839696..142842108-chr3:143048440..143050143,2	K562	blood:
12	chr3:142838518..142840970-chr3:143064617..143066302,2	K562	blood:
13	chr3:142839800..142841734-chr3:142873166..142874850,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241679	TF binding region
ENSG00000241679	CpG island
ENSG00000240012	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000240950	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3438597	chr3:142838687-142841235	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a
8	esv3421903	chr3:142839312-142842010	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142837000-142840400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr3:142837200-142840600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr3:142837400-142840200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:142837400-142840400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:142837400-142840400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:142837400-142840600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:142837600-142840200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:142837600-142840200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:142837600-142840200	Active TSS	Right Atrium	heart
10	chr3:142837600-142840200	Active TSS	K562	blood
11	chr3:142837600-142840400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:142837600-142840400	Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr3:142837600-142840400	Active TSS	Brain Hippocampus Middle	brain
14	chr3:142837600-142840400	Active TSS	Brain Substantia Nigra	brain
15	chr3:142837600-142840400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:142837600-142840400	Active TSS	HSMMtube	muscle
17	chr3:142837600-142840400	Active TSS	NHDF-Ad	bronchial
18	chr3:142837600-142840600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:142837600-142840600	Active TSS	Primary T cells from cord blood	blood
20	chr3:142837600-142840600	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr3:142837600-142840600	Active TSS	NHLF	lung
22	chr3:142837600-142840600	Active TSS	Osteobl	bone
23	chr3:142837600-142840800	Active TSS	Brain Anterior Caudate	brain
24	chr3:142837600-142840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:142837600-142841000	Active TSS	HSMM	muscle
26	chr3:142837600-142841200	Active TSS	Brain Angular Gyrus	brain
27	chr3:142837800-142840200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:142837800-142840200	Active TSS	Ovary	ovary
29	chr3:142837800-142840200	Active TSS	Small Intestine	intestine
30	chr3:142837800-142840200	Active TSS	Spleen	Spleen
31	chr3:142837800-142840400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:142837800-142840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr3:142837800-142840400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
34	chr3:142837800-142840600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:142837800-142840600	Active TSS	Brain Cingulate Gyrus	brain
36	chr3:142837800-142843400	Active TSS	Fetal Kidney	kidney
37	chr3:142838000-142840200	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr3:142838000-142840200	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr3:142838000-142840200	Active TSS	GM12878-XiMat	blood
40	chr3:142838000-142840200	Bivalent/Poised TSS	NHEK	skin
41	chr3:142838000-142840400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:142838000-142840600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:142838200-142840200	Active TSS	Thymus	Thymus
44	chr3:142838200-142840400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
45	chr3:142838200-142840400	Active TSS	HUVEC	blood vessel
46	chr3:142838400-142840200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr3:142838400-142840200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:142838400-142840200	Active TSS	Fetal Thymus	thymus
49	chr3:142838600-142840400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr3:142838800-142840200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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