Variant report

Variant	rs57455059
Chromosome Location	chr12:38451682-38451683
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:38450015..38451840-chr2:133028967..133030976,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ALG10B-6	chr12:38451526-38451849	NONHSAT027672

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11181686	1.00[EUR][1000 genomes]
rs11182039	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182041	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11182093	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11182231	0.89[AMR][1000 genomes]
rs11531287	0.89[ASN][1000 genomes]
rs11534980	0.81[EUR][1000 genomes]
rs11561513	0.87[EUR][1000 genomes]
rs11561516	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12231283	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12232000	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12581348	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581437	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28829386	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3908192	1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57696337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60969787	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72644808	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72644809	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72644810	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72644811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043459	chr12:37857751-38662460	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1050718	chr12:37857751-38757302	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv898972	chr12:37857899-38719455	ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv898973	chr12:37913469-38733094	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv898974	chr12:37913469-38881918	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1035849	chr12:37929227-38640613	ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv898975	chr12:37964922-38499180	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv898976	chr12:37964922-38640613	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv898977	chr12:37969625-38472919	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv898978	chr12:37969625-38624795	Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv1050465	chr12:37987714-38479611	Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv898983	chr12:38015951-38499180	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv898984	chr12:38015951-38553973	Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv898985	chr12:38015951-38856607	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv898986	chr12:38015951-38922227	ZNF genes & repeats Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
16	nsv1048489	chr12:38034346-38452742	Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv1039413	chr12:38053225-38513906	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv2422349	chr12:38103874-38761647	ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	esv2422488	chr12:38103874-39070734	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
20	nsv1054674	chr12:38104736-38452742	Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv898992	chr12:38106133-38959053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv1052762	chr12:38169669-38640955	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1039580	chr12:38169669-38844008	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	nsv1047388	chr12:38169669-38949760	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
25	nsv1047550	chr12:38207030-38908242	Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
26	nsv1035850	chr12:38207030-38912512	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	nsv558570	chr12:38242029-38465461	ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
28	nsv558571	chr12:38242029-38557886	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
29	nsv558572	chr12:38242029-38708549	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
30	nsv469355	chr12:38242029-38851642	Weak transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
31	nsv558573	chr12:38242029-38851642	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
32	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
33	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
34	esv3398964	chr12:38255337-38564698	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
35	nsv1036471	chr12:38279331-38843441	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
36	esv2762974	chr12:38317760-38463513	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
37	nsv469357	chr12:38347638-38865066	Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
38	nsv558580	chr12:38347638-38865066	Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
39	nsv558581	chr12:38373092-38865066	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
40	nsv1039819	chr12:38377445-38482975	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
41	nsv1037285	chr12:38377445-38832352	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
42	nsv1047616	chr12:38377445-38843441	Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
43	nsv1048454	chr12:38377445-38868369	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
44	nsv1049142	chr12:38377445-38872038	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
45	nsv1053589	chr12:38377445-38875511	ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
46	nsv1041670	chr12:38381206-38860567	Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
47	esv2751097	chr12:38385512-38843441	Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
48	nsv1035353	chr12:38424982-38491004	Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
49	nsv899004	chr12:38424982-38730455	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
50	nsv1046762	chr12:38424982-38807781	Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:38442200-38452200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:38449000-38453800	Weak transcription	Right Atrium	heart
3	chr12:38450200-38453800	Weak transcription	Pancreas	Pancrea
4	chr12:38450600-38456600	Weak transcription	Gastric	stomach
5	chr12:38451200-38453400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:38451400-38451800	Enhancers	Hela-S3	cervix
7	chr12:38451600-38451800	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links