Variant report

Variant	rs13425834
Chromosome Location	chr2:78683660-78683661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRTM4-3	chr2:78683574-78683857	NONHSAT071835

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10166453	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10197263	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs10200062	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10203802	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10451628	0.88[EUR][1000 genomes]
rs13411152	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs13422559	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs13425208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13426270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516255	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs1516256	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs1516257	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs1516259	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs1521505	0.86[EUR][1000 genomes]
rs17015316	1.00[CHB][hapmap]
rs17015412	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs55884007	0.90[EUR][1000 genomes]
rs56044358	0.93[EUR][1000 genomes]
rs56114016	0.97[EUR][1000 genomes]
rs56268498	0.88[EUR][1000 genomes]
rs62164665	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62164669	0.92[EUR][1000 genomes]
rs62164671	0.97[EUR][1000 genomes]
rs62164672	0.97[EUR][1000 genomes]
rs62164673	0.97[EUR][1000 genomes]
rs62164674	0.97[EUR][1000 genomes]
rs62164675	0.92[EUR][1000 genomes]
rs62164676	0.97[EUR][1000 genomes]
rs62164691	0.86[EUR][1000 genomes]
rs62164693	0.93[EUR][1000 genomes]
rs62164697	0.93[EUR][1000 genomes]
rs62166119	0.90[EUR][1000 genomes]
rs62166128	0.88[EUR][1000 genomes]
rs62166129	0.88[EUR][1000 genomes]
rs62166131	0.88[EUR][1000 genomes]
rs62166136	0.93[EUR][1000 genomes]
rs62166137	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62166138	0.88[EUR][1000 genomes]
rs62166139	0.97[EUR][1000 genomes]
rs62166142	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62166143	0.95[EUR][1000 genomes]
rs62166144	0.97[EUR][1000 genomes]
rs66969671	0.86[EUR][1000 genomes]
rs6721735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72808856	0.81[EUR][1000 genomes]
rs72808867	0.88[EUR][1000 genomes]
rs72808897	0.97[EUR][1000 genomes]
rs72810614	0.97[EUR][1000 genomes]
rs72810616	0.95[EUR][1000 genomes]
rs72810617	0.97[EUR][1000 genomes]
rs72810620	0.97[EUR][1000 genomes]
rs9309533	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757811	chr2:78126389-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2759068	chr2:78126389-78711032	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014232	chr2:78413760-79034119	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535788	chr2:78413760-79034119	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916498	chr2:78429997-79340383	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv582273	chr2:78432494-78978011	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014484	chr2:78504497-78972453	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1002114	chr2:78511306-78743191	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv535789	chr2:78511306-78743191	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv834271	chr2:78519702-78711032	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv3584761	chr2:78545020-79430628	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv874360	chr2:78546919-78691068	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv998961	chr2:78574081-79150087	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1002687	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv535790	chr2:78575186-78943679	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv874361	chr2:78582650-78691068	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv874362	chr2:78582650-78805852	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv874363	chr2:78608101-78702648	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv428052	chr2:78615333-79075603	Enhancers ZNF genes & repeats Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv874364	chr2:78640246-78857870	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv1007043	chr2:78653616-78796446	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv874365	chr2:78658280-78805852	Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv874366	chr2:78658280-78857870	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv874367	chr2:78658280-78945755	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	esv2763648	chr2:78668935-78736009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
26	nsv874368	chr2:78668935-78805852	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv874369	chr2:78668935-78818453	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	nsv874370	chr2:78668935-79013457	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
29	nsv1004668	chr2:78673888-78797459	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	nsv535791	chr2:78673888-78797459	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:78682400-78683800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:78683400-78742200	Weak transcription	HepG2	liver

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