Variant report

Variant	rs3024993
Chromosome Location	chr6:43743303-43743304
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	POLR2A	chr6:43742213-43744407	K562	blood:	n/a	n/a
2	SMC3	chr6:43736561-43743761	SK-N-SH	brain:	n/a	chr6:43739308-43739322 chr6:43737366-43737380 chr6:43737167-43737181
3	POLR2A	chr6:43737070-43746379	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr6:43742504-43744575	K562	blood:	n/a	n/a
5	POLR2A	chr6:43737291-43756474	K562	blood:	n/a	n/a
6	POLR2A	chr6:43736571-43752619	HepG2	liver:	n/a	n/a
7	HEY1	chr6:43736480-43752618	HepG2	liver:	n/a	chr6:43737671-43737686 chr6:43739793-43739808
8	POLR2A	chr6:43742335-43743505	K562	blood:	n/a	n/a
9	POLR2A	chr6:43742764-43748019	K562	blood:	n/a	n/a
10	EBF1	chr6:43743077-43743367	GM12878	blood:	n/a	n/a
11	STAT1	chr6:43743291-43743374	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:43738927-43752629	HepG2	liver:	n/a	n/a
13	EBF1	chr6:43743014-43743362	GM12878	blood:	n/a	n/a
14	POLR2A	chr6:43736601-43746456	IMR90	lung:	n/a	n/a
15	HEY1	chr6:43743073-43743546	K562	blood:	n/a	n/a
16	POLR2A	chr6:43736458-43765400	U87	brain:	n/a	n/a
17	POLR2A	chr6:43736482-43752553	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:43737208-43745329	HCT-116	colon:	n/a	n/a
19	EBF1	chr6:43741066-43743556	GM12878	blood:	n/a	chr6:43742761-43742772
20	CTCF	chr6:43743160-43743310	AG09309	skin:	n/a	n/a
21	POLR2A	chr6:43736371-43765427	U87	brain:	n/a	n/a
22	CTCF	chr6:43743180-43743330	GM12872	blood:	n/a	n/a
23	RAD21	chr6:43742213-43743677	SK-N-SH	brain:	n/a	n/a
24	POLR2A	chr6:43743239-43743753	PANC-1	pancreas:	n/a	n/a
25	MXI1	chr6:43736453-43743614	SK-N-SH	brain:	n/a	n/a
26	MAZ	chr6:43735419-43745130	IMR90	lung:	n/a	chr6:43739126-43739135 chr6:43736845-43736855 chr6:43739801-43739811 chr6:43739253-43739262 chr6:43739604-43739614 chr6:43739715-43739724 chr6:43737895-43737904 chr6:43739142-43739151
27	POLR2A	chr6:43736623-43760187	U87	brain:	n/a	n/a
28	CHD1	chr6:43736165-43753887	IMR90	lung:	n/a	chr6:43739796-43739806 chr6:43739318-43739328

No.	Distal block	Cell Line	Cell type
1	chr6:43742782..43745224-chr6:44046035..44049278,3	MCF-7	breast:
2	chr6:43742162..43743417-chr6:44046432..44047565,6	K562	blood:
3	chr6:43742777..43745112-chr6:43953190..43954729,2	K562	blood:
4	chr6:43595036..43601855-chr6:43735920..43743852,18	K562	blood:
5	chr6:43592224..43600252-chr6:43737312..43744228,11	MCF-7	breast:
6	chr6:43742830..43744458-chr6:44047475..44049981,2	MCF-7	breast:
7	chr6:43742231..43743744-chr6:43805695..43806498,4	MCF-7	breast:
8	chr6:43591688..43594576-chr6:43742532..43744832,2	K562	blood:
9	chr6:43736441..43745894-chr6:44037513..44049664,39	K562	blood:
10	chr6:43594866..43599640-chr6:43736940..43745540,22	K562	blood:
11	chr6:43730164..43744120-chr6:44034600..44052665,50	K562	blood:
12	chr6:43690346..43692325-chr6:43742986..43744888,2	K562	blood:
13	chr6:43630711..43632822-chr6:43742887..43744413,2	K562	blood:

Variant related genes	Relation type
VEGFA	TF binding region
ENSG00000272114	TF binding region
ENSG00000172432	Chromatin interaction
ENSG00000231881	Chromatin interaction
ENSG00000124688	Chromatin interaction
ENSG00000237686	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs9472122	0.88[AFR][1000 genomes];1.00[AMR][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	nsv869383	chr6:43505094-43752189	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
3	nsv1018626	chr6:43694649-43803732	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv885848	chr6:43732669-43753051	Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:43738200-43744000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr6:43739800-43743400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:43739800-43743400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:43739800-43743600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:43739800-43744000	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr6:43740200-43744400	Enhancers	Primary hematopoietic stem cells	blood
7	chr6:43740200-43748000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:43740200-43752200	Weak transcription	Aorta	Aorta
9	chr6:43740400-43743400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:43740400-43743400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:43740600-43744400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr6:43740600-43745400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
13	chr6:43740800-43743600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:43740800-43743600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:43740800-43743600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:43740800-43755600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:43741200-43743400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:43741200-43743400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:43741400-43743400	Transcr. at gene 5' and 3'	HepG2	liver
20	chr6:43741400-43743600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:43741600-43743400	Transcr. at gene 5' and 3'	Hela-S3	cervix
22	chr6:43741800-43744200	Enhancers	Primary B cells from cord blood	blood
23	chr6:43742000-43743400	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr6:43742000-43743600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr6:43742000-43743600	Enhancers	Small Intestine	intestine
26	chr6:43742200-43743600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:43742200-43743600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:43742200-43743800	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:43742200-43744000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:43742200-43744600	Enhancers	Fetal Thymus	thymus
31	chr6:43742200-43745000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
32	chr6:43742600-43743600	Enhancers	Fetal Kidney	kidney
33	chr6:43742600-43743600	Genic enhancers	NHEK	skin
34	chr6:43742600-43745200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:43742600-43746200	Enhancers	Fetal Heart	heart
36	chr6:43742600-43756400	Weak transcription	Primary T cells from cord blood	blood
37	chr6:43742800-43743400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:43742800-43743400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
39	chr6:43742800-43750200	Genic enhancers	Gastric	stomach
40	chr6:43743000-43743400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:43743000-43743400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:43743000-43743400	Enhancers	Brain Substantia Nigra	brain
43	chr6:43743000-43743400	Enhancers	Fetal Brain Male	brain
44	chr6:43743000-43743600	Enhancers	H1 Cell Line	embryonic stem cell
45	chr6:43743000-43743600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr6:43743000-43743600	Genic enhancers	Colonic Mucosa	Colon
47	chr6:43743000-43743800	Enhancers	Pancreas	Pancrea
48	chr6:43743000-43744000	Enhancers	Brain Angular Gyrus	brain
49	chr6:43743000-43744000	Enhancers	Brain Hippocampus Middle	brain
50	chr6:43743000-43744200	Genic enhancers	Rectal Mucosa Donor 29	rectum

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