Variant report

Variant	rs9823284
Chromosome Location	chr3:45883992-45883993
allele	C/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	MTA3	chr3:45882896-45884096	GM12878	blood:	n/a	n/a
2	CEBPB	chr3:45883257-45884031	MCF-7	breast:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
3	TCF12	chr3:45883168-45884088	ECC-1	luminal epithelium:	n/a	chr3:45883363-45883370
4	MXI1	chr3:45882841-45884011	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr3:45883195-45884049	HCT-116	colon:	n/a	n/a
6	MAX	chr3:45883118-45884158	HCT-116	colon:	n/a	chr3:45883629-45883639
7	MAX	chr3:45883172-45884148	A549	lung:	n/a	chr3:45883629-45883639
8	E2F6	chr3:45883514-45884038	A549	lung:	n/a	n/a
9	E2F6	chr3:45883252-45884142	A549	lung:	n/a	n/a
10	SETDB1	chr3:45883222-45884060	K562	blood:	n/a	n/a
11	GABPA	chr3:45883106-45884267	HL-60	blood:	n/a	chr3:45883710-45883719
12	GTF2F1	chr3:45883531-45883993	Hela-S3	cervix:	n/a	n/a
13	GABPA	chr3:45883329-45884161	MCF-7	breast:	n/a	chr3:45883710-45883719
14	POLR2A	chr3:45883289-45884027	H1-neurons	neurons:	n/a	n/a
15	CEBPB	chr3:45883309-45884107	ECC-1	luminal epithelium:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
16	MXI1	chr3:45882091-45884476	IMR90	lung:	n/a	n/a
17	CBX3	chr3:45883409-45884028	K562	blood:	n/a	n/a
18	MAX	chr3:45883370-45884126	MCF-7	breast:	n/a	chr3:45883629-45883639
19	GABPA	chr3:45882737-45884433	MCF-7	breast:	n/a	chr3:45883018-45883027 chr3:45883016-45883030 chr3:45883710-45883719
20	RCOR1	chr3:45883374-45884031	GM12878	blood:	n/a	n/a
21	GABPA	chr3:45883082-45884217	SK-N-SH	brain:	n/a	chr3:45883710-45883719
22	GABPA	chr3:45883209-45884156	SK-N-SH	brain:	n/a	chr3:45883710-45883719
23	POLR2A	chr3:45883427-45884022	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr3:45883332-45884040	HCT-116	colon:	n/a	n/a
25	GABPA	chr3:45883419-45884105	HL-60	blood:	n/a	chr3:45883710-45883719
26	POU2F2	chr3:45883330-45884015	GM12891	blood:	n/a	chr3:45883648-45883661 chr3:45883648-45883661 chr3:45883648-45883661
27	POLR2A	chr3:45883164-45884138	PBDE	blood:	n/a	n/a
28	POLR2A	chr3:45883043-45884071	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr3:45883090-45884223	HCT-116	colon:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
30	JUND	chr3:45883102-45884113	SK-N-SH	brain:	n/a	n/a
31	E2F6	chr3:45883291-45884058	Hela-S3	cervix:	n/a	n/a
32	MAX	chr3:45883113-45884173	ECC-1	luminal epithelium:	n/a	chr3:45883629-45883639
33	CEBPB	chr3:45883296-45884052	GM12878	blood:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
34	MAX	chr3:45883198-45884068	H1-hESC	embryonic stem cell:	n/a	chr3:45883629-45883639
35	POLR2A	chr3:45883562-45884039	U87	brain:	n/a	n/a
36	ATF2	chr3:45883375-45884048	GM12878	blood:	n/a	n/a
37	MAX	chr3:45883128-45884198	HepG2	liver:	n/a	chr3:45883629-45883639
38	POLR2A	chr3:45883277-45884123	U87	brain:	n/a	n/a
39	GABPA	chr3:45883337-45884103	K562	blood:	n/a	chr3:45883710-45883719
40	MTA3	chr3:45883064-45884020	GM12878	blood:	n/a	n/a
41	CEBPB	chr3:45883040-45884185	HCT-116	colon:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
42	POLR2A	chr3:45883525-45884079	ECC-1	luminal epithelium:	n/a	n/a
43	YY1	chr3:45883273-45884004	GM12878	blood:	n/a	chr3:45883430-45883444
44	GABPA	chr3:45883202-45884114	A549	lung:	n/a	chr3:45883710-45883719
45	HEY1	chr3:45883678-45883995	K562	blood:	n/a	n/a
46	CEBPB	chr3:45883289-45883998	H1-hESC	embryonic stem cell:	n/a	chr3:45883687-45883698 chr3:45883687-45883700 chr3:45883689-45883698 chr3:45883689-45883698 chr3:45883689-45883698
47	MAX	chr3:45883269-45884099	SK-N-SH	brain:	n/a	chr3:45883629-45883639
48	YY1	chr3:45883381-45884047	GM12878	blood:	n/a	chr3:45883430-45883444
49	POLR2A	chr3:45883488-45884058	GM12878	blood:	n/a	n/a
50	POLR2A	chr3:45883379-45884014	GM18505	blood:	n/a	n/a

Variant related genes	Relation type
LZTFL1	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11130077	0.81[ASN][1000 genomes]
rs1129183	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318088	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488370	0.81[ASN][1000 genomes]
rs1883091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883092	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2531756	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2633734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774644	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45558831	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683143	0.96[ASN][1000 genomes]
rs60103812	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61157369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836780	1.00[YRI][hapmap]
rs9844499	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849511	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882270	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 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	chr3:45882200-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:45882200-45884000	Active TSS	Thymus	Thymus
3	chr3:45882200-45884200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr3:45882200-45886600	Strong transcription	Dnd41	blood
5	chr3:45882400-45884000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:45882400-45884000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:45882400-45884200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr3:45882400-45884400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:45882600-45884000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:45882600-45884000	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr3:45882600-45884000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:45882600-45884000	Active TSS	Ovary	ovary
13	chr3:45882600-45884200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:45882600-45884200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:45882600-45884200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr3:45882600-45884200	Active TSS	Right Atrium	heart
17	chr3:45882600-45884200	Active TSS	A549	lung
18	chr3:45882600-45884200	Active TSS	HSMM	muscle
19	chr3:45882600-45884400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:45882800-45884000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:45882800-45884000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:45882800-45884000	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:45882800-45884000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:45882800-45884000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:45882800-45884000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:45882800-45884000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:45882800-45884000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr3:45882800-45884000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:45882800-45884000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:45882800-45884000	Active TSS	Brain Angular Gyrus	brain
31	chr3:45882800-45884000	Active TSS	Esophagus	oesophagus
32	chr3:45882800-45884000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:45882800-45884000	Flanking Active TSS	Placenta	Placenta
34	chr3:45882800-45884000	Active TSS	Gastric	stomach
35	chr3:45882800-45884000	Active TSS	NH-A	brain
36	chr3:45882800-45884000	Active TSS	NHDF-Ad	bronchial
37	chr3:45882800-45884200	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr3:45882800-45884200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr3:45882800-45884200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:45882800-45884200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:45882800-45884200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
42	chr3:45882800-45884200	Active TSS	Colonic Mucosa	Colon
43	chr3:45882800-45884200	Active TSS	Fetal Intestine Small	intestine
44	chr3:45882800-45884200	Active TSS	Fetal Kidney	kidney
45	chr3:45882800-45884200	Active TSS	Psoas Muscle	Psoas
46	chr3:45882800-45884200	Active TSS	Rectal Smooth Muscle	rectum
47	chr3:45882800-45884200	Active TSS	Right Ventricle	heart
48	chr3:45882800-45884200	Active TSS	Stomach Smooth Muscle	stomach
49	chr3:45882800-45884400	Active TSS	Stomach Mucosa	stomach
50	chr3:45882800-45884600	Active TSS	Duodenum Mucosa	Duodenum

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