Variant report

Variant	rs16823639
Chromosome Location	chr2:145090774-145090775
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	MXI1	chr2:145088756-145091117	IMR90	lung:	n/a	n/a
2	MYC	chr2:145088908-145090936	K562	blood:	n/a	chr2:145090315-145090325
3	HCFC1	chr2:145089355-145090809	K562	blood:	n/a	n/a
4	MAX	chr2:145088968-145090984	HepG2	liver:	n/a	chr2:145090315-145090325
5	POLR2A	chr2:145088620-145090777	GM18505	blood:	n/a	n/a
6	TCF12	chr2:145089322-145090780	ECC-1	luminal epithelium:	n/a	chr2:145090737-145090744
7	E2F6	chr2:145089362-145090831	K562	blood:	n/a	chr2:145089796-145089805 chr2:145090248-145090259 chr2:145090249-145090261
8	MYC	chr2:145088808-145090866	K562	blood:	n/a	chr2:145090315-145090325
9	JUND	chr2:145089531-145090871	K562	blood:	n/a	chr2:145090236-145090247 chr2:145090236-145090246
10	E2F6	chr2:145089289-145090792	H1-hESC	embryonic stem cell:	n/a	chr2:145089796-145089805 chr2:145090248-145090259 chr2:145090249-145090261
11	POLR2A	chr2:145088746-145091015	K562	blood:	n/a	n/a
12	BHLHE40	chr2:145088676-145090798	K562	blood:	n/a	chr2:145090272-145090288 chr2:145090248-145090264
13	POLR2A	chr2:145088531-145090794	GM12878	blood:	n/a	n/a
14	UBTF	chr2:145089058-145090866	K562	blood:	n/a	n/a
15	HA-E2F1	chr2:145088947-145090786	MCF-7	breast:	n/a	chr2:145090249-145090260 chr2:145089796-145089805 chr2:145090222-145090233 chr2:145090249-145090261
16	POLR2A	chr2:145088565-145090913	K562	blood:	n/a	n/a
17	POLR2A	chr2:145088608-145090873	Raji	blood:	n/a	n/a
18	GTF2F1	chr2:145090719-145090881	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr2:145089874-145090831	K562	blood:	n/a	n/a
20	TEAD4	chr2:145089470-145090870	K562	blood:	n/a	n/a
21	POLR2A	chr2:145088444-145091000	SK-N-MC	brain:	n/a	n/a
22	MAX	chr2:145089924-145090790	K562	blood:	n/a	chr2:145090315-145090325
23	E2F6	chr2:145090021-145090888	H1-hESC	embryonic stem cell:	n/a	chr2:145090248-145090259 chr2:145090249-145090261
24	E2F4	chr2:145089315-145090825	K562	blood:	n/a	chr2:145090223-145090234 chr2:145089796-145089805 chr2:145090248-145090259 chr2:145090249-145090261
25	POLR2A	chr2:145089253-145090933	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr2:145089219-145090966	A549	lung:	n/a	chr2:145090315-145090325
27	MAX	chr2:145089255-145090859	K562	blood:	n/a	chr2:145090315-145090325
28	CBX3	chr2:145089100-145090898	K562	blood:	n/a	n/a
29	MAX	chr2:145089344-145090867	A549	lung:	n/a	chr2:145090315-145090325
30	RCOR1	chr2:145089527-145090871	K562	blood:	n/a	n/a
31	POLR2A	chr2:145088893-145090777	K562	blood:	n/a	n/a
32	ZNF263	chr2:145089347-145090819	HEK293-T-REx	kidney:	n/a	chr2:145090003-145090024
33	TBP	chr2:145089205-145090879	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:145088522-145090801	PBDE	blood:	n/a	n/a
35	POLR2A	chr2:145088756-145090784	K562	blood:	n/a	n/a
36	MYC	chr2:145088741-145091094	K562	blood:	n/a	chr2:145090315-145090325
37	NRF1	chr2:145090704-145090781	GM12878	blood:	n/a	n/a
38	E2F6	chr2:145090003-145090777	A549	lung:	n/a	chr2:145090248-145090259 chr2:145090249-145090261
39	MAX	chr2:145089508-145090797	A549	lung:	n/a	chr2:145090315-145090325

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:144987319..144988823-chr2:145090215..145092011,2	K562	blood:

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16823629	1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55830030	1.00[AMR][1000 genomes]
rs58046208	1.00[AMR][1000 genomes]
rs60032580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72992109	1.00[AMR][1000 genomes]
rs72992116	1.00[AMR][1000 genomes]
rs72992120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7587100	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription 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	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv948474	chr2:145035890-145436665	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS 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	14 gene(s)	inside rSNPs	diseases
13	nsv1004937	chr2:145079535-145159021	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	esv3339969	chr2:145088932-145091180	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145088400-145090800	Active TSS	Right Atrium	heart
2	chr2:145088400-145091000	Active TSS	NHDF-Ad	bronchial
3	chr2:145088600-145090800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:145088600-145090800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:145088600-145090800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:145088600-145090800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:145088600-145090800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:145088600-145090800	Active TSS	Aorta	Aorta
9	chr2:145088600-145090800	Active TSS	Colonic Mucosa	Colon
10	chr2:145088600-145090800	Active TSS	Right Ventricle	heart
11	chr2:145088600-145091000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr2:145088800-145090800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr2:145088800-145090800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:145088800-145090800	Active TSS	Left Ventricle	heart
15	chr2:145088800-145091000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:145088800-145091000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr2:145089000-145090800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:145089000-145090800	Active TSS	Esophagus	oesophagus
19	chr2:145089000-145090800	Active TSS	Gastric	stomach
20	chr2:145089000-145090800	Active TSS	Lung	lung
21	chr2:145089000-145090800	Active TSS	Placenta Amnion	Placenta Amnion
22	chr2:145089400-145090800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr2:145089400-145090800	Active TSS	Primary B cells from cord blood	blood
24	chr2:145089400-145090800	Active TSS	NHLF	lung
25	chr2:145089400-145091000	Active TSS	Duodenum Mucosa	Duodenum
26	chr2:145090200-145090800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:145090200-145090800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:145090200-145090800	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr2:145090200-145090800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:145090200-145090800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:145090200-145090800	Flanking Active TSS	Dnd41	blood
32	chr2:145090200-145090800	Flanking Active TSS	HUVEC	blood vessel
33	chr2:145090200-145091000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:145090400-145090800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:145090400-145090800	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
36	chr2:145090400-145090800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr2:145090400-145090800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr2:145090400-145090800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr2:145090400-145090800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr2:145090400-145090800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr2:145090400-145090800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr2:145090400-145090800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:145090400-145090800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr2:145090400-145090800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr2:145090400-145090800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr2:145090400-145090800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:145090400-145090800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:145090400-145090800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:145090400-145090800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:145090400-145090800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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