Variant report

Variant	rs563576463
Chromosome Location	chr3:142838768-142838769
allele	A/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	UBTF	chr3:142837331-142839986	K562	blood:	n/a	n/a
2	MXI1	chr3:142837650-142838810	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:142837413-142839052	K562	blood:	n/a	n/a
4	PML	chr3:142837737-142838834	K562	blood:	n/a	n/a
5	POLR2A	chr3:142837303-142839328	K562	blood:	n/a	n/a
6	NRF1	chr3:142838461-142838796	SK-N-SH	brain:	n/a	n/a
7	CREB1	chr3:142837717-142839100	GM12878	blood:	n/a	n/a
8	ZNF263	chr3:142837735-142839609	HEK293-T-REx	kidney:	n/a	chr3:142839428-142839437
9	MAX	chr3:142837797-142838844	A549	lung:	n/a	n/a
10	POLR2A	chr3:142838311-142838837	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:142837773-142841232	GM19193	blood:	n/a	n/a
12	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:142837418-142838863	Raji	blood:	n/a	n/a
14	REST	chr3:142838406-142839406	H1-neurons	neurons:	n/a	chr3:142838875-142838884 chr3:142839356-142839366 chr3:142839020-142839030 chr3:142839154-142839167
15	TAF1	chr3:142838528-142838797	GM12891	blood:	n/a	n/a
16	POLR2A	chr3:142837371-142841744	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:142838327-142838875	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr3:142837450-142838856	K562	blood:	n/a	n/a
20	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
21	E2F4	chr3:142837855-142839159	K562	blood:	n/a	chr3:142838688-142838696 chr3:142838683-142838698 chr3:142838425-142838435 chr3:142838688-142838696 chr3:142838914-142838924 chr3:142838688-142838695 chr3:142838911-142838921 chr3:142838694-142838704 chr3:142838688-142838695 chr3:142838688-142838695 chr3:142838697-142838707 chr3:142838917-142838927 chr3:142838687-142838697 chr3:142838700-142838710
22	MAX	chr3:142837708-142838862	A549	lung:	n/a	n/a
23	TAF1	chr3:142838534-142838822	H1-hESC	embryonic stem cell:	n/a	n/a
24	GABPA	chr3:142837741-142838876	K562	blood:	n/a	chr3:142838115-142838124 chr3:142837992-142837999
25	POLR2A	chr3:142837796-142841213	GM12878	blood:	n/a	n/a
26	PML	chr3:142837665-142840120	GM12878	blood:	n/a	n/a
27	ZEB1	chr3:142838502-142839017	GM12878	blood:	n/a	chr3:142838792-142838801
28	POLR2A	chr3:142837397-142840013	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:142837372-142842950	GM12891	blood:	n/a	n/a
30	POLR2A	chr3:142838523-142838844	H1-hESC	embryonic stem cell:	n/a	n/a
31	ZBTB7A	chr3:142837837-142839574	ECC-1	luminal epithelium:	n/a	n/a
32	POU2F2	chr3:142838508-142838880	GM12878	blood:	n/a	chr3:142838857-142838869
33	POLR2A	chr3:142837824-142840822	GM12878	blood:	n/a	n/a
34	TAF1	chr3:142838315-142838817	K562	blood:	n/a	n/a
35	NFYB	chr3:142838065-142838783	K562	blood:	n/a	n/a
36	POLR2A	chr3:142838257-142839048	U87	brain:	n/a	n/a
37	TBP	chr3:142837414-142838827	K562	blood:	n/a	n/a
38	CHD1	chr3:142838568-142839462	GM12878	blood:	n/a	n/a
39	E2F6	chr3:142838259-142838774	K562	blood:	n/a	chr3:142838688-142838696 chr3:142838683-142838698 chr3:142838425-142838435 chr3:142838688-142838696 chr3:142838688-142838695 chr3:142838694-142838704 chr3:142838688-142838695 chr3:142838688-142838695 chr3:142838697-142838707 chr3:142838687-142838697 chr3:142838700-142838710
40	IRF1	chr3:142838518-142838779	K562	blood:	n/a	n/a
41	TBL1XR1	chr3:142838685-142839000	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:142838052-142838916	HEK293	kidney:	n/a	n/a
43	POLR2A	chr3:142837844-142838863	GM19099	blood:	n/a	n/a
44	EP300	chr3:142838483-142839057	H1-hESC	embryonic stem cell:	n/a	chr3:142838698-142838707 chr3:142838596-142838612 chr3:142838917-142838926 chr3:142838695-142838704 chr3:142838753-142838769 chr3:142838914-142838923
45	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
46	MAX	chr3:142838103-142839488	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:142837371-142840452	GM12892	blood:	n/a	n/a
48	RCOR1	chr3:142838353-142838854	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:142837405-142838836	K562	blood:	n/a	n/a
50	CREB1	chr3:142838368-142838774	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142777135..142778996-chr3:142838578..142841035,2	K562	blood:
2	chr3:142795942..142798929-chr3:142838470..142841083,3	K562	blood:
3	chr3:142760861..142763721-chr3:142838517..142840129,2	K562	blood:
4	chr3:142546469..142548561-chr3:142838535..142840408,2	K562	blood:
5	chr3:142295506..142297981-chr3:142837321..142839389,2	K562	blood:
6	chr3:142719801..142721977-chr3:142838395..142840175,2	K562	blood:
7	chr3:142772025..142774338-chr3:142838383..142839930,2	K562	blood:
8	chr3:142729466..142732055-chr3:142838748..142841571,2	K562	blood:
9	chr3:142755305..142760138-chr3:142835756..142840820,6	K562	blood:
10	chr3:142838518..142840970-chr3:143064617..143066302,2	K562	blood:

Variant related genes	Relation type
ENSG00000241679	TF binding region
ENSG00000163714	Chromatin interaction
ENSG00000240950	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000268129	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142836600-142839200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:142837000-142840400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:142837200-142840600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr3:142837400-142838800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:142837400-142839000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:142837400-142839400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:142837400-142839800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
8	chr3:142837400-142840200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:142837400-142840400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:142837400-142840400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:142837400-142840600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr3:142837600-142839000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr3:142837600-142839400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:142837600-142839600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:142837600-142839800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:142837600-142840200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:142837600-142840200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:142837600-142840200	Active TSS	Right Atrium	heart
19	chr3:142837600-142840200	Active TSS	K562	blood
20	chr3:142837600-142840400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:142837600-142840400	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr3:142837600-142840400	Active TSS	Brain Hippocampus Middle	brain
23	chr3:142837600-142840400	Active TSS	Brain Substantia Nigra	brain
24	chr3:142837600-142840400	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr3:142837600-142840400	Active TSS	HSMMtube	muscle
26	chr3:142837600-142840400	Active TSS	NHDF-Ad	bronchial
27	chr3:142837600-142840600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:142837600-142840600	Active TSS	Primary T cells from cord blood	blood
29	chr3:142837600-142840600	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:142837600-142840600	Active TSS	NHLF	lung
31	chr3:142837600-142840600	Active TSS	Osteobl	bone
32	chr3:142837600-142840800	Active TSS	Brain Anterior Caudate	brain
33	chr3:142837600-142840800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:142837600-142841000	Active TSS	HSMM	muscle
35	chr3:142837600-142841200	Active TSS	Brain Angular Gyrus	brain
36	chr3:142837800-142838800	Active TSS	Colonic Mucosa	Colon
37	chr3:142837800-142839000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:142837800-142839000	Active TSS	Right Ventricle	heart
39	chr3:142837800-142839000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
40	chr3:142837800-142839200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr3:142837800-142839200	Active TSS	HMEC	breast
42	chr3:142837800-142839400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr3:142837800-142839400	Active TSS	Esophagus	oesophagus
44	chr3:142837800-142839400	Active TSS	Gastric	stomach
45	chr3:142837800-142839400	Active TSS	Left Ventricle	heart
46	chr3:142837800-142839400	Active TSS	Lung	lung
47	chr3:142837800-142839400	Bivalent/Poised TSS	A549	lung
48	chr3:142837800-142839600	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:142837800-142839600	Active TSS	Rectal Smooth Muscle	rectum
50	chr3:142837800-142839600	Active TSS	Sigmoid Colon	Sigmoid Colon

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