Variant report

Variant	rs72684499
Chromosome Location	chr1:45672933-45672934
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	GATA2	chr1:45672574-45672960	HUVEC	blood vessel:	n/a	n/a
2	ZKSCAN1	chr1:45671739-45673236	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr1:45672587-45673296	SH-SY5Y	brain:	n/a	n/a
4	SMC3	chr1:45672300-45673055	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr1:45670219-45673038	SK-N-SH	brain:	n/a	n/a
6	GATA2	chr1:45672554-45672963	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45480075..45485962-chr1:45670647..45674355,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPDL-1	chr1:45672409-45675890	NONHSAT002922

Variant related genes	Relation type
ZSWIM5	TF binding region
ENSG00000126088	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10157175	0.84[AMR][1000 genomes]
rs10157807	0.84[AMR][1000 genomes]
rs1152028	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809934	0.84[AMR][1000 genomes]
rs11810829	0.84[AMR][1000 genomes]
rs1226732	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1226750	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612575	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173208	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969084	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995403	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105460	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346685	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346686	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346688	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346689	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346692	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346703	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346704	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346709	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346710	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346711	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346718	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346720	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346725	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346726	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346730	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346735	0.84[AFR][1000 genomes]
rs409082	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412055	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415614	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660835	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55826381	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55842174	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884892	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55996819	0.84[AMR][1000 genomes]
rs56165953	0.84[AMR][1000 genomes]
rs57805650	0.84[ASN][1000 genomes]
rs60506423	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61574129	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6429556	0.89[ASN][1000 genomes]
rs6693885	0.89[ASN][1000 genomes]
rs72684425	0.81[ASN][1000 genomes]
rs72684426	0.81[ASN][1000 genomes]
rs72684447	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684454	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684481	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684482	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684488	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72684496	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72686404	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72686415	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686418	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686419	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686420	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686421	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686423	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72686425	0.84[AMR][1000 genomes]
rs72686431	0.84[AMR][1000 genomes]
rs72686433	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
2	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
3	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
5	esv3365432	chr1:45670715-45673638	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3444099	chr1:45670790-45673738	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45668000-45673800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:45669400-45673200	Active TSS	Brain Angular Gyrus	brain
3	chr1:45669400-45673400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:45670000-45673200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:45670000-45673400	Active TSS	Ovary	ovary
6	chr1:45670400-45673200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:45670600-45673000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:45670600-45673000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr1:45670600-45673200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:45670600-45673200	Active TSS	Colonic Mucosa	Colon
11	chr1:45670800-45673000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:45670800-45673000	Active TSS	Pancreas	Pancrea
13	chr1:45671000-45673000	Active TSS	Aorta	Aorta
14	chr1:45671000-45673000	Active TSS	Right Ventricle	heart
15	chr1:45671200-45673000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:45671200-45673000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr1:45671200-45673000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:45671200-45673000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr1:45671200-45673200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr1:45671400-45673000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
21	chr1:45671400-45673200	Active TSS	Brain Germinal Matrix	brain
22	chr1:45671400-45673200	Active TSS	Fetal Intestine Large	intestine
23	chr1:45671600-45673000	Flanking Bivalent TSS/Enh	Dnd41	blood
24	chr1:45672200-45673000	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
25	chr1:45672400-45673000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:45672400-45673000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr1:45672400-45673000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
28	chr1:45672400-45673000	Active TSS	Right Atrium	heart
29	chr1:45672400-45673000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
30	chr1:45672400-45673200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr1:45672400-45673200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:45672400-45673200	Flanking Active TSS	HUVEC	blood vessel
33	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:45672600-45673000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr1:45672600-45673000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:45672600-45673000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
39	chr1:45672600-45673000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:45672600-45673000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:45672600-45673000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:45672600-45673000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr1:45672600-45673000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:45672600-45673000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:45672600-45673000	Flanking Active TSS	Liver	Liver
48	chr1:45672600-45673000	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr1:45672600-45673000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr1:45672600-45673000	Flanking Active TSS	Fetal Brain Male	brain

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