Variant report

Variant	rs12460025
Chromosome Location	chr19:22318230-22318231
allele	A/G
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	chr19:22318107-22318751	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PCGF7P	TF binding region
ZNF92P2	TF binding region

Extended variants
information (count: 126 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10403375	0.82[EUR][1000 genomes]
rs10411854	0.84[EUR][1000 genomes]
rs10412921	0.84[EUR][1000 genomes]
rs10417143	0.80[EUR][1000 genomes]
rs10418058	0.84[EUR][1000 genomes]
rs10419384	0.84[EUR][1000 genomes]
rs10419666	0.84[EUR][1000 genomes]
rs10419926	0.84[EUR][1000 genomes]
rs10425845	0.84[EUR][1000 genomes]
rs12459032	0.84[EUR][1000 genomes]
rs1378915	0.84[EUR][1000 genomes]
rs1526883	0.84[EUR][1000 genomes]
rs17554725	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1830172	0.84[EUR][1000 genomes]
rs1830173	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1852417	0.81[EUR][1000 genomes]
rs1852418	0.83[EUR][1000 genomes]
rs1852427	0.84[EUR][1000 genomes]
rs1852428	0.84[EUR][1000 genomes]
rs1918161	0.84[EUR][1000 genomes]
rs1918162	0.84[EUR][1000 genomes]
rs2204581	0.82[EUR][1000 genomes]
rs2360002	0.83[EUR][1000 genomes]
rs281174	0.80[EUR][1000 genomes]
rs281176	0.84[EUR][1000 genomes]
rs281177	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs281178	0.84[EUR][1000 genomes]
rs281179	0.84[EUR][1000 genomes]
rs281180	0.84[EUR][1000 genomes]
rs281181	0.84[EUR][1000 genomes]
rs281182	0.84[EUR][1000 genomes]
rs281183	0.84[EUR][1000 genomes]
rs281184	0.80[EUR][1000 genomes]
rs281185	0.82[EUR][1000 genomes]
rs281186	0.83[EUR][1000 genomes]
rs28760999	0.84[EUR][1000 genomes]
rs28790613	0.84[EUR][1000 genomes]
rs2884867	0.84[EUR][1000 genomes]
rs371540	0.84[EUR][1000 genomes]
rs381995	0.84[EUR][1000 genomes]
rs3855858	0.84[EUR][1000 genomes]
rs3934143	0.84[EUR][1000 genomes]
rs399307	0.84[EUR][1000 genomes]
rs400419	0.83[EUR][1000 genomes]
rs400661	0.84[EUR][1000 genomes]
rs409627	0.84[EUR][1000 genomes]
rs412658	0.84[EUR][1000 genomes]
rs414983	0.83[EUR][1000 genomes]
rs416928	0.83[EUR][1000 genomes]
rs427343	0.83[EUR][1000 genomes]
rs436431	0.84[EUR][1000 genomes]
rs4371283	0.84[EUR][1000 genomes]
rs446754	0.84[EUR][1000 genomes]
rs447533	0.83[EUR][1000 genomes]
rs451793	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs451905	0.84[EUR][1000 genomes]
rs456246	0.82[EUR][1000 genomes]
rs457504	0.85[EUR][1000 genomes]
rs4584959	0.84[EUR][1000 genomes]
rs459539	0.85[EUR][1000 genomes]
rs4614861	0.80[EUR][1000 genomes]
rs461661	0.85[EUR][1000 genomes]
rs461804	0.85[EUR][1000 genomes]
rs462671	0.85[EUR][1000 genomes]
rs4932951	0.82[CHB][hapmap]
rs4932963	0.80[EUR][1000 genomes]
rs56284384	0.81[EUR][1000 genomes]
rs62112446	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs682866	0.84[EUR][1000 genomes]
rs7248898	0.83[ASN][1000 genomes]
rs7253425	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7343076	0.84[EUR][1000 genomes]
rs7343077	0.84[EUR][1000 genomes]
rs7343144	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7343146	0.84[EUR][1000 genomes]
rs8105545	0.84[EUR][1000 genomes]
rs8106346	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:49 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	esv2760532	chr19:22236219-22355753	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv1055550	chr19:22242042-22554079	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
22	nsv520741	chr19:22250136-22321256	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv470135	chr19:22250137-22321256	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv525240	chr19:22250912-23216667	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
25	nsv911436	chr19:22252823-22338142	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	nsv1063392	chr19:22253673-22320009	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv1058539	chr19:22253673-22337607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv1061426	chr19:22253673-22342973	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv1061285	chr19:22253673-22352744	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv1059044	chr19:22253673-22353360	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
31	esv2762029	chr19:22253673-22353372	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
32	nsv1067333	chr19:22253673-22355741	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv1056653	chr19:22253864-22407089	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
34	nsv543952	chr19:22253864-22407089	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
35	nsv911437	chr19:22256060-22364620	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
36	nsv1066390	chr19:22258101-22321219	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
37	nsv543953	chr19:22258101-22321219	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
38	nsv1062108	chr19:22258101-22408495	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
39	nsv543954	chr19:22258101-22408495	ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
40	nsv1060342	chr19:22263236-22321219	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
41	nsv543955	chr19:22263236-22321219	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
42	nsv978900	chr19:22269235-22358448	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
43	esv3347466	chr19:22269939-22416232	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
44	nsv911438	chr19:22278121-22346403	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
45	nsv1056971	chr19:22280694-22321219	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
46	nsv543956	chr19:22280694-22321219	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
47	nsv963027	chr19:22310707-22321259	Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
48	esv2752392	chr19:22316560-22520360	ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
49	nsv432040	chr19:22316560-22704860	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs12460025	ZNF676	cis	cerebellum	SCAN
rs12460025	ZNF626	cis	parietal	SCAN
rs12460025	ZNF257	cis	Adipose Subcutaneous	GTEx
rs12460025	ZNF257	cis	lung	GTEx
rs12460025	ZNF257	cis	cerebellum	SCAN
rs12460025	ARRDC2	cis	parietal	SCAN
rs12460025	HAPLN4	cis	parietal	SCAN
rs12460025	ZNF682	cis	parietal	SCAN
rs12460025	ZNF257	cis	parietal	SCAN
rs12460025	ZNF676	cis	Thyroid	GTEx
rs12460025	ZNF257	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22317600-22319000	ZNF genes & repeats	Liver	Liver
2	chr19:22317800-22318400	Active TSS	Fetal Heart	heart

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