Variant report

Variant	rs2732453
Chromosome Location	chr12:48719793-48719794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr12:48719246-48719823	A549	lung:	n/a	n/a
2	SETDB1	chr12:48719512-48719966	U2OS	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48719777-48719827	IMR90	lung:	fetal
2	chr12:48719777-48719827	SK-N-SH_RA	brain:	n/a
3	chr12:48719777-48719827	HL-60	blood:	n/a
4	chr12:48719777-48719827	U87	brain:	n/a
5	chr12:48719777-48719827	HAEpiC	amniotic membrane:	n/a
6	chr12:48719777-48719827	SAEC	small airway:	n/a
7	chr12:48719777-48719827	MCF10A-Er-Src	breast:	n/a
8	chr12:48719777-48719827	PANC-1	pancreas:	n/a
9	chr12:48719777-48719827	HIPEpiC	eye:	n/a
10	chr12:48719777-48719827	PFSK-1	brain:	n/a
11	chr12:48719777-48719827	Jurkat	blood:	n/a
12	chr12:48719777-48719827	AG09309	skin:	n/a
13	chr12:48719777-48719827	CMK	blood:	n/a
14	chr12:48719777-48719827	HCF	heart:	n/a
15	chr12:48719777-48719827	HEK293	kidney:	embryo
16	chr12:48719777-48719827	HPAEpiC	pulmonary alveolar:	n/a
17	chr12:48719777-48719827	AG04450	lung:	fetal
18	chr12:48719777-48719827	HRPEpiC	eye:	n/a
19	chr12:48719777-48719827	Hepatocyte	liver:	n/a
20	chr12:48719777-48719827	HUVEC	blood vessel:	n/a
21	chr12:48719777-48719827	NB4	blood:	n/a
22	chr12:48719777-48719827	HCPEpiC	choroid plexus:	n/a
23	chr12:48719777-48719827	MCF-7	breast:	n/a
24	chr12:48719777-48719827	ProgFib	skin:	n/a
25	chr12:48719777-48719827	HCT-116	colon:	n/a
26	chr12:48719777-48719827	HRCEpiC	kidney:	n/a
27	chr12:48719777-48719827	SKMC	muscle:	n/a
28	chr12:48719777-48719827	Hela-S3	cervix:	n/a
29	chr12:48719777-48719827	T-47D	breast:	n/a
30	chr12:48719777-48719827	GM12891	blood:	n/a
31	chr12:48719777-48719827	K562	blood:	n/a
32	chr12:48719777-48719827	BE2_C	brain:	n/a
33	chr12:48719777-48719827	A549	lung:	n/a
34	chr12:48719777-48719827	SK-N-MC	brain:	n/a
35	chr12:48719777-48719827	ovcar-3	ovarian:	n/a
36	chr12:48719777-48719827	BJ	skin:	n/a
37	chr12:48719777-48719827	H1-hESC	embryonic stem cell:	embryo
38	chr12:48719777-48719827	NH-A	brain:	n/a
39	chr12:48719777-48719827	AG04449	skin:	fetal
40	chr12:48719777-48719827	HEEpiC	esophagus:	n/a
41	chr12:48719777-48719827	GM12892	blood:	n/a
42	chr12:48719777-48719827	LNCaP	prostate:	n/a
43	chr12:48719777-48719827	AoSMC	blood vessel:	n/a
44	chr12:48719777-48719827	NHDF-neo	bronchial:	n/a
45	chr12:48719777-48719827	RPTEC	kidney:	n/a
46	chr12:48719777-48719827	HepG2	liver:	n/a
47	chr12:48719777-48719827	HNPCEpiC	eye:	n/a
48	chr12:48719777-48719827	AG10803	skin:	n/a
49	chr12:48719777-48719827	Caco-2	colon:	n/a
50	chr12:48719777-48719827	SK-N-SH	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48718530..48720177-chr12:48742678..48744445,2	MCF-7	breast:

No data

Variant related genes	Relation type
H1FNT	TF binding region
H1FNT	CpG island
ENSG00000167528	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1061986	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1107654	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11168468	0.85[EUR][1000 genomes]
rs11168474	0.85[EUR][1000 genomes]
rs11168484	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12828309	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12829841	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1387259	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1387260	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1489108	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1542707	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1552550	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1601985	0.82[AMR][1000 genomes]
rs2054905	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2409003	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409004	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450994	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2450996	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2468943	0.87[EUR][1000 genomes]
rs2468946	0.81[EUR][1000 genomes]
rs2468949	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634670	0.84[AMR][1000 genomes]
rs2634676	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634678	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634680	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2634681	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634682	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634684	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2634686	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634688	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634689	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2634691	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634692	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2634693	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2634694	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2634697	0.84[AMR][1000 genomes]
rs2732441	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732445	0.82[AMR][1000 genomes]
rs2732448	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732454	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2732457	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2732461	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2732462	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732466	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2732479	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732480	0.83[ASN][1000 genomes]
rs2732481	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732484	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732486	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2732488	0.82[AMR][1000 genomes]
rs2956703	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2956710	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34286639	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6580662	0.86[EUR][1000 genomes]
rs7307566	0.83[EUR][1000 genomes]
rs7966829	0.85[EUR][1000 genomes]
rs923397	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active 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	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv899064	chr12:48664989-48721832	Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv826362	chr12:48693048-48768853	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2732453	H1FNT	cis	Muscle Skeletal	GTEx
rs2732453	H1FNT	cis	Artery Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
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