Variant report

Variant	rs59460700
Chromosome Location	chr1:228328964-228328965
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:49)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:49 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:228327199-228329184	GM12878	blood:	n/a	n/a
2	UBTF	chr1:228327292-228329537	K562	blood:	n/a	n/a
3	MAX	chr1:228327196-228329894	K562	blood:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
4	JUN	chr1:228327040-228329256	K562	blood:	n/a	chr1:228327920-228327933
5	POLR2A	chr1:228327060-228329092	K562	blood:	n/a	n/a
6	MAZ	chr1:228328858-228329358	K562	blood:	n/a	n/a
7	MYC	chr1:228328963-228329788	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr1:228327097-228329751	IMR90	lung:	n/a	n/a
9	RCOR1	chr1:228328843-228329004	K562	blood:	n/a	n/a
10	WRNIP1	chr1:228328437-228330112	GM12878	blood:	n/a	n/a
11	ELF1	chr1:228327146-228329456	GM12878	blood:	n/a	chr1:228328261-228328273 chr1:228327699-228327711 chr1:228328106-228328115
12	POLR2A	chr1:228327209-228329992	K562	blood:	n/a	n/a
13	MXI1	chr1:228327403-228329679	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:228327346-228328972	GM12878	blood:	n/a	n/a
15	MXI1	chr1:228327052-228329702	SK-N-SH	brain:	n/a	n/a
16	MYC	chr1:228327336-228329755	K562	blood:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
17	IRF1	chr1:228328744-228329246	K562	blood:	n/a	chr1:228329022-228329043
18	RUNX3	chr1:228328828-228329216	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:228327198-228329161	GM12891	blood:	n/a	n/a
20	POLR2A	chr1:228327235-228329827	K562	blood:	n/a	n/a
21	IRF1	chr1:228327247-228329497	K562	blood:	n/a	chr1:228327834-228327848 chr1:228327875-228327889 chr1:228328731-228328745 chr1:228329022-228329043 chr1:228327694-228327708 chr1:228328263-228328277
22	POLR2A	chr1:228328947-228329683	K562	blood:	n/a	n/a
23	RUNX3	chr1:228328677-228329321	GM12878	blood:	n/a	n/a
24	CHD1	chr1:228327017-228329831	IMR90	lung:	n/a	n/a
25	MYC	chr1:228328933-228329707	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr1:228327114-228332328	IMR90	lung:	n/a	n/a
27	IRF1	chr1:228328855-228329194	K562	blood:	n/a	chr1:228329022-228329043
28	POLR2A	chr1:228327239-228329943	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:228327324-228329296	GM18505	blood:	n/a	n/a
30	MYC	chr1:228328861-228329652	K562	blood:	n/a	n/a
31	POLR2A	chr1:228327129-228329167	GM19193	blood:	n/a	n/a
32	NR2F2	chr1:228327128-228329051	K562	blood:	n/a	n/a
33	MXI1	chr1:228327323-228329650	GM12878	blood:	n/a	n/a
34	MAZ	chr1:228327249-228329314	IMR90	lung:	n/a	chr1:228328264-228328274 chr1:228327695-228327705
35	CBX3	chr1:228328899-228329679	K562	blood:	n/a	n/a
36	POLR2A	chr1:228328848-228329026	HUVEC	blood vessel:	n/a	n/a
37	STAT5A	chr1:228328728-228329102	GM12878	blood:	n/a	n/a
38	CCNT2	chr1:228328903-228329268	K562	blood:	n/a	n/a
39	MAX	chr1:228328947-228329450	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:228327142-228329234	GM12892	blood:	n/a	n/a
41	CHD1	chr1:228327337-228329387	GM12878	blood:	n/a	n/a
42	SIN3A	chr1:228328758-228329245	GM12878	blood:	n/a	n/a
43	MTA3	chr1:228328910-228329442	GM12878	blood:	n/a	n/a
44	POLR2A	chr1:228327370-228330398	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:228328816-228329565	K562	blood:	n/a	n/a
46	CHD2	chr1:228328855-228329237	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:228327172-228329094	H1-hESC	embryonic stem cell:	n/a	n/a
48	PML	chr1:228327130-228328977	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:228327083-228330995	GM12878	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228327365..228329534-chr1:228645028..228646794,2	MCF-7	breast:
2	chr1:228267667..228275106-chr1:228326600..228331394,10	K562	blood:
3	chr1:228269915..228273320-chr1:228326449..228329096,4	K562	blood:
4	chr1:228328826..228331169-chr1:228395338..228396936,2	K562	blood:
5	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
6	chr1:228290240..228294197-chr1:228325970..228329742,3	MCF-7	breast:
7	chr1:228269306..228272326-chr1:228326148..228329488,5	MCF-7	breast:
8	chr1:228294222..228297212-chr1:228327852..228330069,2	MCF-7	breast:
9	chr1:228288649..228293430-chr1:228325997..228329591,7	K562	blood:
10	chr1:228327593..228329181-chr1:228644179..228646860,2	MCF-7	breast:
11	chr1:228326695..228329093-chr1:228572036..228574543,2	K562	blood:
12	chr1:228284520..228292111-chr1:228324853..228335412,14	K562	blood:
13	chr1:228286712..228292079-chr1:228327501..228330420,5	MCF-7	breast:
14	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
15	chr1:228327795..228330213-chr1:228593794..228595426,3	K562	blood:
16	chr1:228326053..228331395-chr1:228462710..228467617,6	K562	blood:
17	chr1:228328463..228331528-chr1:228462308..228464210,3	K562	blood:
18	chr1:228326723..228329419-chr1:228644101..228647035,3	K562	blood:
19	chr1:228269794..228271921-chr1:228327972..228330804,3	MCF-7	breast:
20	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GJC2-2	chr1:228328825-228329534	NONHSAT009981

No data

Variant related genes	Relation type
GUK1	TF binding region
ENSG00000162910	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000264944	Chromatin interaction
ENSG00000270104	Chromatin interaction
ENSG00000154358	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000143793	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000269934	Chromatin interaction
ENSG00000231563	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11541554	1.00[AMR][1000 genomes]
rs15109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2231717	1.00[AMR][1000 genomes]
rs55662277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55686465	1.00[AMR][1000 genomes]
rs55904630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55923168	1.00[AMR][1000 genomes]
rs56003736	1.00[AMR][1000 genomes]
rs56029925	1.00[AMR][1000 genomes]
rs56080014	1.00[AMR][1000 genomes]
rs56137152	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56280722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56285667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56377909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56386805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56410225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58045861	1.00[AMR][1000 genomes]
rs59478442	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60628313	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61100243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61230585	1.00[AMR][1000 genomes]
rs61401568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140910	1.00[AMR][1000 genomes]
rs74140916	1.00[AMR][1000 genomes]
rs74140919	1.00[AMR][1000 genomes]
rs74140923	1.00[AMR][1000 genomes]
rs74140953	1.00[AMR][1000 genomes]
rs74140954	1.00[AMR][1000 genomes]
rs74140955	1.00[AMR][1000 genomes]
rs74140956	1.00[AMR][1000 genomes]
rs74140957	1.00[AMR][1000 genomes]
rs74140963	1.00[AMR][1000 genomes]
rs74140967	1.00[AMR][1000 genomes]
rs74140969	1.00[AMR][1000 genomes]
rs74140970	1.00[AMR][1000 genomes]
rs74140971	1.00[AMR][1000 genomes]
rs74140972	1.00[AMR][1000 genomes]
rs74140973	1.00[AMR][1000 genomes]
rs74140974	1.00[AMR][1000 genomes]
rs74140975	1.00[AMR][1000 genomes]
rs74140976	1.00[AMR][1000 genomes]
rs74140977	1.00[AMR][1000 genomes]
rs74140978	1.00[AMR][1000 genomes]
rs74140980	1.00[AMR][1000 genomes]
rs74140981	1.00[AMR][1000 genomes]
rs74140982	1.00[AMR][1000 genomes]
rs74140986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74140999	1.00[AMR][1000 genomes]
rs74141000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74141002	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142608	1.00[AFR][1000 genomes]
rs74142610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142616	1.00[AFR][1000 genomes]
rs74142618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142624	0.85[AFR][1000 genomes]
rs74142626	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142627	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142629	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142630	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74142638	0.85[AFR][1000 genomes]
rs74142640	0.85[AFR][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	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
5	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
6	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
7	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
8	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
9	nsv827019	chr1:228314167-228651020	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
10	nsv873256	chr1:228322826-228359775	Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
11	nsv873257	chr1:228322826-228412106	Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
12	esv3398542	chr1:228326754-228329302	Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv549288	chr1:228327659-228363750	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
14	nsv549289	chr1:228327999-228371098	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228327000-228329000	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:228327000-228329000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:228327000-228329200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:228327000-228329200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:228327000-228329400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:228327000-228329400	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:228327200-228329000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:228327200-228329000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:228327200-228329000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:228327200-228329000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:228327200-228329000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:228327200-228329000	Active TSS	Fetal Kidney	kidney
13	chr1:228327200-228329000	Active TSS	Left Ventricle	heart
14	chr1:228327200-228329000	Active TSS	Lung	lung
15	chr1:228327200-228329000	Active TSS	A549	lung
16	chr1:228327200-228329000	Active TSS	HSMMtube	muscle
17	chr1:228327200-228329000	Active TSS	NHLF	lung
18	chr1:228327200-228329000	Active TSS	Osteobl	bone
19	chr1:228327200-228329200	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:228327200-228329200	Active TSS	Esophagus	oesophagus
21	chr1:228327200-228329200	Active TSS	Ovary	ovary
22	chr1:228327200-228329200	Active TSS	Psoas Muscle	Psoas
23	chr1:228327200-228329200	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr1:228327200-228329400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:228327200-228329400	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:228327200-228329400	Active TSS	NHDF-Ad	bronchial
27	chr1:228327400-228329000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:228327400-228329000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:228327400-228329000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:228327400-228329000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr1:228327400-228329000	Active TSS	Aorta	Aorta
32	chr1:228327400-228329000	Active TSS	Thymus	Thymus
33	chr1:228327400-228329000	Active TSS	Spleen	Spleen
34	chr1:228327400-228329200	Active TSS	NHEK	skin
35	chr1:228327400-228329400	Active TSS	Gastric	stomach
36	chr1:228327400-228329400	Active TSS	Small Intestine	intestine
37	chr1:228327400-228329600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:228327400-228329600	Active TSS	Muscle Satellite Cultured Cells	--
39	chr1:228327400-228329600	Active TSS	GM12878-XiMat	blood
40	chr1:228327400-228329600	Active TSS	HSMM	muscle
41	chr1:228327600-228329000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:228327600-228329000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:228328000-228329000	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:228328000-228329400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:228328000-228329600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:228328200-228329000	Active TSS	Right Atrium	heart
47	chr1:228328200-228329200	Bivalent/Poised TSS	HepG2	liver
48	chr1:228328200-228329600	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr1:228328200-228330200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr1:228328400-228329200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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