Variant report

Variant	rs394457
Chromosome Location	chr19:22230428-22230429
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	CEBPB	chr19:22229978-22231113	A549	lung:	n/a	n/a
2	CEBPB	chr19:22229982-22231755	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ZNF257	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10401697	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10416159	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10419899	0.80[EUR][1000 genomes]
rs11670558	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1849000	0.86[AMR][1000 genomes]
rs1849001	0.86[AMR][1000 genomes]
rs1849003	0.81[AMR][1000 genomes]
rs1849006	0.83[AMR][1000 genomes]
rs1859092	0.81[AMR][1000 genomes]
rs1859093	0.86[AMR][1000 genomes]
rs1987570	0.96[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1987974	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1987975	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1988427	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1988501	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2007506	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2079062	0.83[AMR][1000 genomes]
rs2079064	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2097733	0.81[AMR][1000 genomes]
rs2106870	0.87[EUR][1000 genomes]
rs2158107	0.83[AMR][1000 genomes]
rs2188971	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2214296	0.81[AMR][1000 genomes]
rs2214297	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs2214301	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2262908	0.91[AMR][1000 genomes]
rs2359810	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2359812	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2359813	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2359814	0.82[EUR][1000 genomes]
rs2359815	0.96[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2522089	0.81[AMR][1000 genomes]
rs2522090	0.86[AMR][1000 genomes]
rs2522093	0.81[AMR][1000 genomes]
rs2522094	0.83[AMR][1000 genomes]
rs2522095	0.86[AMR][1000 genomes]
rs2522096	0.87[CEU][hapmap];0.84[AMR][1000 genomes]
rs2522101	0.81[AMR][1000 genomes]
rs2522103	0.86[AMR][1000 genomes]
rs2666438	0.85[AMR][1000 genomes]
rs2666440	0.86[AMR][1000 genomes]
rs2666442	0.84[AMR][1000 genomes]
rs2666448	0.85[AMR][1000 genomes]
rs2666449	0.81[AMR][1000 genomes]
rs2666450	0.81[AMR][1000 genomes]
rs2666453	0.86[AMR][1000 genomes]
rs28635943	0.86[YRI][hapmap]
rs366863	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs367280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408687	0.81[CHB][hapmap]
rs411020	0.81[CHB][hapmap]
rs415291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416312	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs417066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs417628	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422344	0.81[CHB][hapmap]
rs423284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423926	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378732	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4592778	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4932723	1.00[CEU][hapmap]
rs507994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548059	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6511305	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6511306	0.83[EUR][1000 genomes]
rs6511307	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6511308	0.83[EUR][1000 genomes]
rs6511321	0.93[YRI][hapmap]
rs7247121	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7248488	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7249472	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7258834	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73019876	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8101183	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs8103214	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8108152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8108160	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8108535	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8108807	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8111955	0.87[EUR][1000 genomes]
rs8112395	0.87[EUR][1000 genomes]
rs9304993	1.00[CEU][hapmap]
rs9653156	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv833785	chr19:22082143-22263312	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1058678	chr19:22084265-22288686	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1059225	chr19:22084265-22301003	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv2754060	chr19:22086241-22567144	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv432039	chr19:22086260-22704860	ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	esv3384540	chr19:22089182-22316805	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv3326382	chr19:22112592-22509135	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	esv3392637	chr19:22135121-22332040	ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv961196	chr19:22142802-22258858	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv3514246	chr19:22145480-22348690	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	esv3514247	chr19:22145480-22348690	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv3495704	chr19:22149379-22352547	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3495705	chr19:22149379-22352547	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
17	nsv469674	chr19:22154515-22344992	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv436253	chr19:22188479-22385212	ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	esv3360126	chr19:22209871-23199213	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
20	esv3507723	chr19:22209960-22315161	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	esv3507724	chr19:22209960-22315161	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	esv3333410	chr19:22213338-23199725	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
23	nsv911434	chr19:22215457-22438069	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
24	esv3424104	chr19:22223429-22436512	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv1064904	chr19:22229835-22408495	Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv543951	chr19:22229835-22408495	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs394457	AC003973.1	cis	Thyroid	GTEx
rs394457	ZNF257	cis	parietal	SCAN
rs394457	AC003973.1	cis	Artery Tibial	GTEx

Chromatin state (count:0 , 50 per page) page:

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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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