Variant report

Variant	rs4701947
Chromosome Location	chr5:12654571-12654572
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:12653349..12655490-chr5:12663314..12666064,2	K562	blood:
2	chr5:12647069..12649041-chr5:12653810..12656965,3	K562	blood:
3	chr5:12652956..12655094-chr5:12656361..12658712,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTNND2-3	chr5:12653170-12654688	NONHSAT100517

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10059816	0.82[EUR][1000 genomes]
rs10061998	0.89[ASN][1000 genomes]
rs10077071	0.92[ASN][1000 genomes]
rs12520290	0.87[ASN][1000 genomes]
rs12522873	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12652084	0.82[EUR][1000 genomes]
rs12658823	0.91[ASN][1000 genomes]
rs12659603	0.84[EUR][1000 genomes]
rs13182649	0.87[ASN][1000 genomes]
rs13182975	0.92[ASN][1000 genomes]
rs4133113	0.84[EUR][1000 genomes]
rs4352596	0.84[EUR][1000 genomes]
rs4610458	0.81[EUR][1000 genomes]
rs4701945	0.82[EUR][1000 genomes]
rs4702896	0.84[EUR][1000 genomes]
rs55696989	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57761512	0.84[EUR][1000 genomes]
rs58190884	0.85[EUR][1000 genomes]
rs58985097	0.84[EUR][1000 genomes]
rs59010274	0.82[EUR][1000 genomes]
rs60350744	0.84[EUR][1000 genomes]
rs60387048	0.82[EUR][1000 genomes]
rs60883509	0.86[EUR][1000 genomes]
rs60926621	0.81[EUR][1000 genomes]
rs61060472	0.86[ASN][1000 genomes]
rs62347654	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62347656	0.85[EUR][1000 genomes]
rs62347657	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62349198	0.82[EUR][1000 genomes]
rs62349204	0.84[EUR][1000 genomes]
rs62349205	0.81[EUR][1000 genomes]
rs62349206	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62349207	0.84[EUR][1000 genomes]
rs62349208	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62349209	0.83[EUR][1000 genomes]
rs62349212	0.85[EUR][1000 genomes]
rs62349214	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6554726	0.82[EUR][1000 genomes]
rs6554742	0.85[EUR][1000 genomes]
rs67133766	0.84[EUR][1000 genomes]
rs67603770	0.85[EUR][1000 genomes]
rs6868308	0.85[EUR][1000 genomes]
rs6887002	0.85[EUR][1000 genomes]
rs6887427	0.82[EUR][1000 genomes]
rs6892313	0.85[EUR][1000 genomes]
rs71601425	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs71601426	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72733281	0.84[EUR][1000 genomes]
rs7447992	0.80[EUR][1000 genomes]
rs7709041	0.87[ASN][1000 genomes]
rs7731055	0.82[EUR][1000 genomes]
rs7737817	0.82[EUR][1000 genomes]
rs9312808	0.86[ASN][1000 genomes]
rs9687355	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9687365	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9716878	0.86[EUR][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	nsv1025096	chr5:12049731-12778382	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537660	chr5:12049731-12778382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv427711	chr5:12285375-12747819	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv917255	chr5:12310838-12929427	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv915585	chr5:12336874-12849583	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv880509	chr5:12360373-12778299	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv520673	chr5:12389751-12733263	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv880760	chr5:12389751-12921838	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv817507	chr5:12404458-12902524	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1034539	chr5:12417170-12711376	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1017679	chr5:12457731-13393269	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv537667	chr5:12457731-13393269	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1023123	chr5:12488303-12686616	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv1034776	chr5:12502153-12748961	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv537668	chr5:12502153-12748961	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv881369	chr5:12510848-12765292	Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv530415	chr5:12513605-13227760	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
18	nsv1023197	chr5:12520949-12735744	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv1020732	chr5:12520949-12778382	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv537669	chr5:12520949-12778382	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv1016102	chr5:12525748-12669535	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv881078	chr5:12527430-12670184	Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
23	nsv880533	chr5:12528965-12778299	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
24	nsv880994	chr5:12528965-12804565	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
25	nsv428463	chr5:12536206-12747819	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
26	nsv597157	chr5:12536870-12670184	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
27	nsv830206	chr5:12541346-12703682	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv1025507	chr5:12556935-12778382	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	nsv537670	chr5:12556935-12778382	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv881678	chr5:12566885-12697079	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
31	nsv880638	chr5:12566885-12765292	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
32	nsv881084	chr5:12566885-12778299	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
33	nsv461978	chr5:12566885-13328289	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
34	nsv1029412	chr5:12588949-12778382	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
35	nsv461979	chr5:12599348-12670184	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
36	nsv461980	chr5:12599348-12670184	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
37	nsv597158	chr5:12599348-12670184	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
38	nsv880794	chr5:12599348-12765292	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
39	nsv880985	chr5:12606091-12780942	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
40	nsv597159	chr5:12616793-13032839	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
41	nsv1018954	chr5:12619289-12734092	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
42	nsv597160	chr5:12641719-12853444	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
43	nsv881450	chr5:12643099-12783665	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
44	nsv880784	chr5:12643099-12834853	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
45	nsv881088	chr5:12652832-12804565	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:12636600-12659200	Weak transcription	K562	blood
2	chr5:12636800-12655600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr5:12644600-12657000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:12644600-12658400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr5:12644800-12654800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr5:12650400-12658800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:12651000-12654600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:12652800-12654600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:12653200-12663200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:12654400-12662800	Strong transcription	HUES64 Cell Line	embryonic stem cell

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