Variant report

Variant	rs56130300
Chromosome Location	chr1:152757273-152757274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10157301	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048535	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494277	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10788847	0.89[ASN][1000 genomes]
rs11205086	0.89[ASN][1000 genomes]
rs11578927	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581045	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11582063	0.89[ASN][1000 genomes]
rs11585409	0.89[ASN][1000 genomes]
rs11586156	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587012	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587180	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094874	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239774	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725760	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728274	0.89[ASN][1000 genomes]
rs12747888	0.89[ASN][1000 genomes]
rs12754243	0.89[ASN][1000 genomes]
rs1412541	0.89[ASN][1000 genomes]
rs1412548	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1591077	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17661905	0.89[ASN][1000 genomes]
rs1888964	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339381	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879458	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34384421	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35274012	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35393920	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36012879	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41268484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353097	0.89[ASN][1000 genomes]
rs4539140	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845473	1.00[ASN][1000 genomes]
rs4845474	1.00[ASN][1000 genomes]
rs4845482	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55683499	0.89[ASN][1000 genomes]
rs56180022	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61812714	1.00[ASN][1000 genomes]
rs6587706	0.82[EUR][1000 genomes]
rs7524281	0.81[EUR][1000 genomes]
rs7539924	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:45 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv1004884	chr1:152724514-152780522	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv1005867	chr1:152744949-152768688	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv1010895	chr1:152744949-152776743	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv79	chr1:152746435-152773598	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
18	nsv2910	chr1:152746435-152774414	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
19	nsv1014190	chr1:152747126-152778861	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv1001012	chr1:152749733-152763057	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1004508	chr1:152749733-152768688	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv997705	chr1:152749733-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv998888	chr1:152749733-152776743	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv1001721	chr1:152750256-152768688	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
26	nsv1009988	chr1:152750256-152773905	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
27	nsv1003849	chr1:152750506-152768688	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv1001837	chr1:152750506-152773905	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
29	nsv1009915	chr1:152750658-152768688	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv1010924	chr1:152750658-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
31	nsv1011430	chr1:152750710-152773905	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
32	nsv1002796	chr1:152751225-152763057	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv1000650	chr1:152751225-152768688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
34	nsv1009758	chr1:152751225-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
35	esv1813620	chr1:152751946-152774632	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
36	esv1799962	chr1:152751946-152778711	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
37	esv1836202	chr1:152754630-152763057	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
38	nsv1011877	chr1:152754630-152767741	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
39	nsv1001998	chr1:152754630-152767951	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
40	nsv1003430	chr1:152754630-152768688	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
41	nsv1007168	chr1:152754630-152773905	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
42	esv3501633	chr1:152754928-152772360	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
43	esv3501634	chr1:152754928-152772360	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
44	nsv1004337	chr1:152756296-152768688	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
45	nsv1001922	chr1:152756774-152768347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56130300	LCE1E	cis	Skin Sun Exposed Lower leg	GTEx
rs56130300	LCE1D	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152755800-152758200	Weak transcription	NHEK	skin
2	chr1:152755800-152758400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:152756000-152758200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152756000-152758200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:152756000-152758200	Weak transcription	HMEC	breast
6	chr1:152757200-152757400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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