Variant report

Variant	rs61812714
Chromosome Location	chr1:152708298-152708299
allele	A/C
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	CTCF	chr1:152708240-152708390	AG04449	skin:	n/a	chr1:152708311-152708329
2	CTCF	chr1:152708245-152708417	GM19240	blood:	n/a	chr1:152708311-152708329
3	CTCF	chr1:152708220-152708370	GM12875	blood:	n/a	chr1:152708311-152708329
4	CTCF	chr1:152708165-152708653	A549	lung:	n/a	chr1:152708311-152708329
5	CTCF	chr1:152708280-152708430	GM12869	blood:	n/a	chr1:152708311-152708329
6	CTCF	chr1:152708121-152708465	K562	blood:	n/a	chr1:152708311-152708329
7	CTCF	chr1:152708240-152708390	GM12865	blood:	n/a	chr1:152708311-152708329
8	CTCF	chr1:152708280-152708430	GM06990	blood:	n/a	chr1:152708311-152708329
9	RAD21	chr1:152708172-152708426	Hela-S3	cervix:	n/a	chr1:152708311-152708323 chr1:152708309-152708328
10	CTCF	chr1:152708240-152708390	GM12872	blood:	n/a	chr1:152708311-152708329
11	CTCF	chr1:152708240-152708390	WERI-Rb-1	eye:	n/a	chr1:152708311-152708329
12	RAD21	chr1:152708223-152708379	SK-N-SH_RA	brain:	n/a	chr1:152708311-152708323 chr1:152708309-152708328
13	CTCF	chr1:152708260-152708410	HRPEpiC	eye:	n/a	chr1:152708311-152708329
14	CTCF	chr1:152708217-152708422	GM12878	blood:	n/a	chr1:152708311-152708329
15	CTCF	chr1:152708197-152708446	NHEK	skin:	n/a	chr1:152708311-152708329
16	CTCF	chr1:152708222-152708432	K562	blood:	n/a	chr1:152708311-152708329
17	CTCF	chr1:152708233-152708405	GM12892	blood:	n/a	chr1:152708311-152708329
18	MYC	chr1:152708182-152708417	MCF10A-Er-Src	breast:	n/a	chr1:152708269-152708279
19	CTCF	chr1:152708240-152708390	GM12871	blood:	n/a	chr1:152708311-152708329
20	CTCF	chr1:152708241-152708385	SK-N-SH_RA	brain:	n/a	chr1:152708311-152708329
21	CTCF	chr1:152708260-152708410	HepG2	liver:	n/a	chr1:152708311-152708329
22	MAZ	chr1:152707899-152708414	HepG2	liver:	n/a	chr1:152708269-152708279
23	CTCF	chr1:152708210-152708432	MCF-7	breast:	n/a	chr1:152708311-152708329
24	CTCF	chr1:152708249-152708416	LNCaP	prostate:	n/a	chr1:152708311-152708329
25	CTCF	chr1:152708200-152708350	AG10803	skin:	n/a	chr1:152708311-152708329
26	CTCF	chr1:152708240-152708390	AG10803	skin:	n/a	chr1:152708311-152708329
27	CTCF	chr1:152708220-152708370	AG04449	skin:	n/a	chr1:152708311-152708329
28	ZNF143	chr1:152708258-152708458	GM12878	blood:	n/a	n/a
29	CTCF	chr1:152708260-152708410	HMEC	breast:	n/a	chr1:152708311-152708329
30	SMC3	chr1:152708188-152708349	GM12878	blood:	n/a	chr1:152708313-152708327
31	CTCF	chr1:152708240-152708390	HEEpiC	esophagus:	n/a	chr1:152708311-152708329
32	CTCF	chr1:152708217-152708428	Fibrobl	skin:	n/a	chr1:152708311-152708329
33	CTCF	chr1:152708220-152708370	SK-N-SH_RA	brain:	n/a	chr1:152708311-152708329
34	CTCF	chr1:152708204-152708448	MCF-7	breast:	n/a	chr1:152708311-152708329
35	MYC	chr1:152708148-152708549	MCF10A-Er-Src	breast:	n/a	chr1:152708269-152708279
36	CTCF	chr1:152708228-152708411	Hela-S3	cervix:	n/a	chr1:152708311-152708329
37	CTCF	chr1:152708200-152708350	GM12870	blood:	n/a	chr1:152708311-152708329
38	CTCF	chr1:152708280-152708430	GM12868	blood:	n/a	chr1:152708311-152708329
39	RAD21	chr1:152708111-152708523	MCF-7	breast:	n/a	chr1:152708311-152708323 chr1:152708309-152708328
40	CTCF	chr1:152708240-152708390	GM12864	blood:	n/a	chr1:152708311-152708329
41	RAD21	chr1:152708085-152708528	A549	lung:	n/a	chr1:152708311-152708323 chr1:152708309-152708328
42	CTCF	chr1:152708185-152708430	K562	blood:	n/a	chr1:152708311-152708329
43	CTCF	chr1:152708180-152708330	HUVEC	blood vessel:	n/a	chr1:152708311-152708329
44	CTCF	chr1:152708240-152708390	Caco-2	colon:	n/a	chr1:152708311-152708329
45	CTCF	chr1:152708280-152708430	A549	lung:	n/a	chr1:152708311-152708329
46	CTCF	chr1:152708220-152708370	GM12872	blood:	n/a	chr1:152708311-152708329
47	CTCF	chr1:152708260-152708410	GM12878	blood:	n/a	chr1:152708311-152708329
48	CTCF	chr1:152708220-152708370	HMF	breast:	n/a	chr1:152708311-152708329
49	CTCF	chr1:152708200-152708350	SK-N-SH_RA	brain:	n/a	chr1:152708311-152708329
50	CTCF	chr1:152708200-152708350	HUVEC	blood vessel:	n/a	chr1:152708311-152708329

No.	Distal block	Cell Line	Cell type
1	chr1:152626165..152627303-chr1:152707558..152708767,8	MCF-7	breast:
2	chr1:152626212..152627124-chr1:152707916..152708805,6	MCF-7	breast:
3	chr1:152469656..152470449-chr1:152707864..152708774,3	MCF-7	breast:
4	chr1:152699751..152702293-chr1:152707659..152709621,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229713	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10157301	1.00[ASN][1000 genomes]
rs1048535	1.00[ASN][1000 genomes]
rs10494277	1.00[ASN][1000 genomes]
rs10788847	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10888512	0.91[EUR][1000 genomes]
rs10888514	0.92[EUR][1000 genomes]
rs11205086	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11205091	0.91[EUR][1000 genomes]
rs11578927	1.00[ASN][1000 genomes]
rs11582063	0.89[ASN][1000 genomes]
rs11585409	0.89[ASN][1000 genomes]
rs11586156	1.00[ASN][1000 genomes]
rs11587012	1.00[ASN][1000 genomes]
rs11587180	1.00[ASN][1000 genomes]
rs12094874	1.00[ASN][1000 genomes]
rs12239774	1.00[ASN][1000 genomes]
rs12725760	1.00[ASN][1000 genomes]
rs12728274	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12747888	0.89[ASN][1000 genomes]
rs12754243	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1332498	0.90[EUR][1000 genomes]
rs1332500	0.91[EUR][1000 genomes]
rs1412541	0.89[ASN][1000 genomes]
rs17661905	0.89[ASN][1000 genomes]
rs1888963	0.92[EUR][1000 genomes]
rs1888964	1.00[ASN][1000 genomes]
rs2339381	1.00[ASN][1000 genomes]
rs2879458	1.00[ASN][1000 genomes]
rs34384421	1.00[ASN][1000 genomes]
rs35274012	1.00[ASN][1000 genomes]
rs35393920	1.00[ASN][1000 genomes]
rs36012879	0.95[ASN][1000 genomes]
rs3814350	0.91[EUR][1000 genomes]
rs41268484	1.00[ASN][1000 genomes]
rs4353097	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4539140	1.00[ASN][1000 genomes]
rs4845318	0.90[EUR][1000 genomes]
rs4845466	0.90[EUR][1000 genomes]
rs4845467	0.90[EUR][1000 genomes]
rs4845468	0.90[EUR][1000 genomes]
rs4845469	0.90[EUR][1000 genomes]
rs4845473	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845482	1.00[ASN][1000 genomes]
rs55683499	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56130300	1.00[ASN][1000 genomes]
rs56180022	1.00[ASN][1000 genomes]
rs6698553	0.91[EUR][1000 genomes]
rs6701365	0.91[EUR][1000 genomes]
rs6701376	0.91[EUR][1000 genomes]
rs7534164	0.90[EUR][1000 genomes]
rs7539924	0.89[ASN][1000 genomes]
rs7545543	0.90[EUR][1000 genomes]
rs873775	0.91[EUR][1000 genomes]
rs944682	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv33483	chr1:152550269-152775526	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv547891	chr1:152556085-152770446	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv469873	chr1:152563260-152713616	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv482518	chr1:152563260-152713616	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
10	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
11	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	esv3692902	chr1:152669367-152732567	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	esv34854	chr1:152671913-152756806	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv818478	chr1:152672005-152734796	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
17	esv2756865	chr1:152682708-152739226	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	esv2763813	chr1:152687058-152780522	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs61812714	LCE1E	cis	Skin Sun Exposed Lower leg	GTEx
rs61812714	LCE1D	cis	Skin Sun Exposed Lower leg	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
chromosomal regions: chr1:12345-34567

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