Variant report

Variant	rs2143416
Chromosome Location	chr1:186653765-186653766
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:186653734-186653774	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:186653723-186653773	SK-N-SH	brain:	n/a
2	chr1:186653723-186653773	GM06990	blood:	n/a
3	chr1:186653723-186653773	NH-A	brain:	n/a
4	chr1:186653723-186653773	HEK293	kidney:	embryo
5	chr1:186653723-186653773	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:186653723-186653773	MCF-7	breast:	n/a
7	chr1:186653723-186653773	IMR90	lung:	fetal
8	chr1:186653723-186653773	PrEC	prostate:	n/a
9	chr1:186653723-186653773	LNCaP	prostate:	n/a
10	chr1:186653723-186653773	PANC-1	pancreas:	n/a
11	chr1:186653723-186653773	Caco-2	colon:	n/a
12	chr1:186653723-186653773	HAEpiC	amniotic membrane:	n/a
13	chr1:186653723-186653773	NB4	blood:	n/a
14	chr1:186653723-186653773	MCF10A-Er-Src	breast:	n/a
15	chr1:186653723-186653773	HIPEpiC	eye:	n/a
16	chr1:186653723-186653773	AG10803	skin:	n/a
17	chr1:186653723-186653773	U87	brain:	n/a
18	chr1:186653723-186653773	T-47D	breast:	n/a
19	chr1:186653723-186653773	AoSMC	blood vessel:	n/a
20	chr1:186653723-186653773	HepG2	liver:	n/a
21	chr1:186653723-186653773	Hepatocyte	liver:	n/a
22	chr1:186653723-186653773	K562	blood:	n/a
23	chr1:186653723-186653773	HEEpiC	esophagus:	n/a
24	chr1:186653723-186653773	HCF	heart:	n/a
25	chr1:186653723-186653773	HL-60	blood:	n/a
26	chr1:186653723-186653773	AG09309	skin:	n/a
27	chr1:186653723-186653773	CMK	blood:	n/a
28	chr1:186653723-186653773	RPTEC	kidney:	n/a
29	chr1:186653723-186653773	SKMC	muscle:	n/a
30	chr1:186653723-186653773	GM12892	blood:	n/a
31	chr1:186653723-186653773	BJ	skin:	n/a
32	chr1:186653723-186653773	PFSK-1	brain:	n/a
33	chr1:186653723-186653773	BE2_C	brain:	n/a
34	chr1:186653723-186653773	ProgFib	skin:	n/a
35	chr1:186653723-186653773	AG04449	skin:	fetal
36	chr1:186653723-186653773	NT2-D1	testis:	n/a
37	chr1:186653723-186653773	HRE	kidney:	n/a
38	chr1:186653723-186653773	HRCEpiC	kidney:	n/a
39	chr1:186653723-186653773	SK-N-SH_RA	brain:	n/a
40	chr1:186653723-186653773	HMEC	breast:	n/a
41	chr1:186653723-186653773	GM12878	blood:	n/a
42	chr1:186653723-186653773	A549	lung:	n/a
43	chr1:186653723-186653773	ECC-1	luminal epithelium:	n/a
44	chr1:186653723-186653773	HUVEC	blood vessel:	n/a
45	chr1:186653723-186653773	GM19239	blood:	n/a
46	chr1:186653723-186653773	SAEC	small airway:	n/a
47	chr1:186653723-186653773	ovcar-3	ovarian:	n/a
48	chr1:186653723-186653773	NHBE	bronchial:	n/a
49	chr1:186653723-186653773	HCM	heart:	n/a
50	chr1:186653723-186653773	Jurkat	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:186652649..186655604-chr1:186657308..186658935,2	MCF-7	breast:

No data

Variant related genes	Relation type
PTGS2	TF binding region
PTGS2	CpG island

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10798048	0.86[CEU][hapmap]
rs10911876	0.86[CEU][hapmap]
rs10911878	0.86[CEU][hapmap]
rs10911886	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap]
rs10911900	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911901	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911903	0.84[ASN][1000 genomes]
rs10911904	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs10911905	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs10911907	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911908	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911909	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10911910	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911911	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1119066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1119230	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1119231	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583191	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11584118	0.84[ASN][1000 genomes]
rs12057695	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12064238	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076624	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12081510	1.00[CHB][hapmap]
rs12084433	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089049	0.84[ASN][1000 genomes]
rs12401885	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12402603	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12404145	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs12405541	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12409744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474596	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16825675	0.80[AFR][1000 genomes]
rs20417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs20432	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066826	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2143417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179555	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2383515	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383516	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2383529	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28469836	0.80[EUR][1000 genomes]
rs2891247	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4422959	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4648250	0.82[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs4648276	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs4648306	0.84[ASN][1000 genomes]
rs4648308	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5275	0.84[ASW][hapmap]
rs60203808	0.82[EUR][1000 genomes]
rs61532952	0.84[ASN][1000 genomes]
rs6425038	0.81[AFR][1000 genomes]
rs66494422	0.84[ASN][1000 genomes]
rs6665419	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6666199	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685280	1.00[ASN][1000 genomes]
rs6698048	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67804662	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67816471	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68096880	0.84[ASN][1000 genomes]
rs689465	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72721568	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7512750	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[MEX][hapmap]
rs7533973	0.82[EUR][1000 genomes]
rs7539054	0.82[AFR][1000 genomes]
rs964571	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783017	0.84[ASN][1000 genomes]
rs9783052	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv2762854	chr1:186547101-186847574	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv470750	chr1:186642429-186700959	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv548403	chr1:186642429-186700959	Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv466261	chr1:186652395-186742947	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv548405	chr1:186652395-186742947	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186651600-186657000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:186653200-186654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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