Variant report

Variant	rs12713231
Chromosome Location	chr2:53105695-53105696
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:53105695-53105745	PrEC	prostate:	n/a
2	chr2:53105695-53105745	Hela-S3	cervix:	n/a
3	chr2:53105695-53105745	AoSMC	blood vessel:	n/a
4	chr2:53105695-53105745	SK-N-SH_RA	brain:	n/a
5	chr2:53105695-53105745	GM12892	blood:	n/a
6	chr2:53105695-53105745	PANC-1	pancreas:	n/a
7	chr2:53105695-53105745	HCM	heart:	n/a
8	chr2:53105695-53105745	AG09309	skin:	n/a
9	chr2:53105695-53105745	GM12891	blood:	n/a
10	chr2:53105695-53105745	HRPEpiC	eye:	n/a
11	chr2:53105695-53105745	GM06990	blood:	n/a
12	chr2:53105695-53105745	MCF-7	breast:	n/a
13	chr2:53105695-53105745	GM12878	blood:	n/a
14	chr2:53105695-53105745	U87	brain:	n/a
15	chr2:53105695-53105745	HRE	kidney:	n/a
16	chr2:53105695-53105745	HMEC	breast:	n/a
17	chr2:53105695-53105745	IMR90	lung:	fetal
18	chr2:53105695-53105745	SK-N-MC	brain:	n/a
19	chr2:53105695-53105745	A549	lung:	n/a
20	chr2:53105695-53105745	MCF10A-Er-Src	breast:	n/a
21	chr2:53105695-53105745	Hepatocyte	liver:	n/a
22	chr2:53105695-53105745	AG04450	lung:	fetal
23	chr2:53105695-53105745	HIPEpiC	eye:	n/a
24	chr2:53105695-53105745	H1-hESC	embryonic stem cell:	embryo
25	chr2:53105695-53105745	Jurkat	blood:	n/a
26	chr2:53105695-53105745	NHBE	bronchial:	n/a
27	chr2:53105695-53105745	NT2-D1	testis:	n/a
28	chr2:53105695-53105745	ProgFib	skin:	n/a
29	chr2:53105695-53105745	ECC-1	luminal epithelium:	n/a
30	chr2:53105695-53105745	LNCaP	prostate:	n/a
31	chr2:53105695-53105745	NHDF-neo	bronchial:	n/a
32	chr2:53105695-53105745	ovcar-3	ovarian:	n/a
33	chr2:53105695-53105745	HUVEC	blood vessel:	n/a
34	chr2:53105695-53105745	PFSK-1	brain:	n/a
35	chr2:53105695-53105745	BJ	skin:	n/a
36	chr2:53105695-53105745	HEEpiC	esophagus:	n/a
37	chr2:53105695-53105745	HNPCEpiC	eye:	n/a
38	chr2:53105695-53105745	HAEpiC	amniotic membrane:	n/a
39	chr2:53105695-53105745	BE2_C	brain:	n/a
40	chr2:53105695-53105745	GM19239	blood:	n/a
41	chr2:53105695-53105745	RPTEC	kidney:	n/a
42	chr2:53105695-53105745	AG09319	gingival:	n/a
43	chr2:53105695-53105745	HCT-116	colon:	n/a
44	chr2:53105695-53105745	Caco-2	colon:	n/a
45	chr2:53105695-53105745	HRCEpiC	kidney:	n/a
46	chr2:53105695-53105745	AG10803	skin:	n/a
47	chr2:53105695-53105745	HepG2	liver:	n/a
48	chr2:53105695-53105745	NH-A	brain:	n/a
49	chr2:53105695-53105745	HCF	heart:	n/a
50	chr2:53105695-53105745	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53103066..53106486-chr2:53106611..53109718,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232668	CpG island

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10164801	0.91[EUR][1000 genomes]
rs10164868	0.90[EUR][1000 genomes]
rs10167421	0.91[EUR][1000 genomes]
rs10168840	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10173886	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10179810	0.91[EUR][1000 genomes]
rs10187465	0.90[ASN][1000 genomes]
rs10191273	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10203699	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10206560	0.90[EUR][1000 genomes]
rs10208858	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10865272	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12475542	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12477231	0.90[EUR][1000 genomes]
rs12614959	0.90[EUR][1000 genomes]
rs12617374	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12617738	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618983	0.90[EUR][1000 genomes]
rs12713227	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713228	0.91[EUR][1000 genomes]
rs12713229	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12713230	0.91[EUR][1000 genomes]
rs12713232	0.92[EUR][1000 genomes]
rs12713233	0.91[EUR][1000 genomes]
rs12990843	0.92[EUR][1000 genomes]
rs13002328	0.90[EUR][1000 genomes]
rs13003962	0.92[EUR][1000 genomes]
rs13030509	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376563	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1376567	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1376569	0.90[EUR][1000 genomes]
rs1376570	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1451455	0.92[EUR][1000 genomes]
rs1451456	0.91[EUR][1000 genomes]
rs1451458	0.90[EUR][1000 genomes]
rs1451460	0.90[EUR][1000 genomes]
rs1597653	0.93[EUR][1000 genomes]
rs1597654	0.82[ASN][1000 genomes]
rs17504530	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1828337	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1828338	0.86[EUR][1000 genomes]
rs1839770	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839771	0.90[EUR][1000 genomes]
rs1864534	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356680	0.92[EUR][1000 genomes]
rs2356681	0.92[EUR][1000 genomes]
rs36130286	0.85[EUR][1000 genomes]
rs4525730	0.92[EUR][1000 genomes]
rs6545310	0.93[EUR][1000 genomes]
rs6715847	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6715857	0.92[EUR][1000 genomes]
rs6725912	0.92[EUR][1000 genomes]
rs6746666	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6754205	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6754423	0.92[EUR][1000 genomes]
rs67939368	0.90[EUR][1000 genomes]
rs724859	0.92[EUR][1000 genomes]
rs724860	0.92[EUR][1000 genomes]
rs74181216	0.91[EUR][1000 genomes]
rs7577692	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998380	chr2:52891706-53222155	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	esv2763631	chr2:52910862-53169629	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006244	chr2:52958322-53169617	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1005813	chr2:52959769-53114865	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1010978	chr2:52959769-53249951	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1014068	chr2:52960353-53169617	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv520722	chr2:53039770-53421015	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1010237	chr2:53072736-53116413	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv581978	chr2:53091691-53227749	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
10	nsv874136	chr2:53101066-53218774	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53094400-53108600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53102600-53108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:53104400-53107200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:53105400-53107600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:53105600-53108200	Weak transcription	A549	lung
6	chr2:53105600-53121800	Weak transcription	Pancreas	Pancrea

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