Variant report

Variant	rs1815925
Chromosome Location	chr18:12093301-12093302
allele	C/T
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	ZNF384	chr18:12092812-12093330	K562	blood:	n/a	n/a
2	RAD21	chr18:12092643-12093307	HCT-116	colon:	n/a	chr18:12093048-12093062 chr18:12092903-12092917 chr18:12093052-12093064 chr18:12092904-12092923 chr18:12093046-12093060
3	RAD21	chr18:12092637-12093320	HCT-116	colon:	n/a	chr18:12093048-12093062 chr18:12092903-12092917 chr18:12093052-12093064 chr18:12092904-12092923 chr18:12093046-12093060
4	CTCF	chr18:12092594-12093313	HCT-116	colon:	n/a	chr18:12092906-12092914 chr18:12092904-12092920 chr18:12093049-12093062 chr18:12092905-12092926 chr18:12092903-12092921

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12092391..12093318-chr18:12246451..12247616,5	K562	blood:
2	chr18:12092426..12095170-chr18:12097480..12099654,2	K562	blood:

Variant related genes	Relation type
ENSG00000267478	TF binding region
ANKRD62	TF binding region
ENSG00000200827	Chromatin interaction
ENSG00000267663	Chromatin interaction

Extended variants
information (count: 192 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs11080540	0.96[AFR][1000 genomes]
rs11872277	0.82[EUR][1000 genomes]
rs11872729	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11875081	0.82[EUR][1000 genomes]
rs11875970	0.82[EUR][1000 genomes]
rs11876652	0.82[EUR][1000 genomes]
rs11876665	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11876694	0.81[EUR][1000 genomes]
rs11876698	0.82[EUR][1000 genomes]
rs11877166	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12604417	0.80[EUR][1000 genomes]
rs12607922	0.93[AFR][1000 genomes]
rs12953431	0.82[EUR][1000 genomes]
rs12953485	0.83[EUR][1000 genomes]
rs12953958	0.83[EUR][1000 genomes]
rs12954230	0.82[EUR][1000 genomes]
rs12955316	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12958791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963290	0.81[EUR][1000 genomes]
rs12963518	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12965571	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12965804	0.83[EUR][1000 genomes]
rs12965831	0.83[EUR][1000 genomes]
rs12965945	0.83[EUR][1000 genomes]
rs12966234	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12966286	0.82[EUR][1000 genomes]
rs12969917	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12970450	0.83[EUR][1000 genomes]
rs12970461	0.83[EUR][1000 genomes]
rs13381564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1942851	0.82[EUR][1000 genomes]
rs1942852	0.82[EUR][1000 genomes]
rs1986750	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1986751	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2006690	0.83[EUR][1000 genomes]
rs2849402	0.83[EUR][1000 genomes]
rs2849404	0.82[EUR][1000 genomes]
rs2849405	0.83[EUR][1000 genomes]
rs2849414	0.83[EUR][1000 genomes]
rs2849415	0.83[EUR][1000 genomes]
rs2849416	0.82[EUR][1000 genomes]
rs2849418	0.82[EUR][1000 genomes]
rs2851900	0.83[EUR][1000 genomes]
rs2851903	0.82[EUR][1000 genomes]
rs2851906	0.82[EUR][1000 genomes]
rs2851922	0.83[EUR][1000 genomes]
rs2851923	0.84[AMR][1000 genomes]
rs28567958	0.82[EUR][1000 genomes]
rs28648884	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28790031	0.83[AMR][1000 genomes]
rs34036584	0.82[EUR][1000 genomes]
rs4239305	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4261610	0.81[EUR][1000 genomes]
rs4296321	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4299212	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4303617	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4306582	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4321255	0.83[EUR][1000 genomes]
rs4321257	0.83[AMR][1000 genomes]
rs4327115	0.80[EUR][1000 genomes]
rs4337367	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4359510	0.83[EUR][1000 genomes]
rs4399596	0.81[EUR][1000 genomes]
rs4399597	0.82[EUR][1000 genomes]
rs4402627	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4416083	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4417605	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417606	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4419117	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4456573	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4464145	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4480870	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4516292	0.83[EUR][1000 genomes]
rs4519391	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4528648	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4538071	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4569357	0.80[EUR][1000 genomes]
rs4572475	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4617931	0.83[EUR][1000 genomes]
rs4621045	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4643402	0.82[EUR][1000 genomes]
rs4796944	0.83[EUR][1000 genomes]
rs4796945	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4796946	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4796947	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797612	0.82[EUR][1000 genomes]
rs4797613	0.83[EUR][1000 genomes]
rs4797616	0.83[EUR][1000 genomes]
rs4797617	0.83[EUR][1000 genomes]
rs4797618	0.83[EUR][1000 genomes]
rs4797623	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4797624	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4797625	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4797631	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797632	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797633	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4797634	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4797636	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4797637	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4797640	0.84[AMR][1000 genomes]
rs56966010	0.93[AFR][1000 genomes]
rs57512036	0.82[EUR][1000 genomes]
rs62097608	0.80[EUR][1000 genomes]
rs62097613	0.84[EUR][1000 genomes]
rs6505710	0.83[EUR][1000 genomes]
rs6505712	0.83[EUR][1000 genomes]
rs6505715	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6505717	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6505720	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6505725	0.82[EUR][1000 genomes]
rs7227857	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7230733	0.82[EUR][1000 genomes]
rs7231001	0.83[EUR][1000 genomes]
rs7236715	0.83[EUR][1000 genomes]
rs7237502	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7237877	0.83[EUR][1000 genomes]
rs7239346	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7239947	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7240093	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7242225	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7242326	0.83[EUR][1000 genomes]
rs7242541	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7242561	0.83[EUR][1000 genomes]
rs7242892	0.83[EUR][1000 genomes]
rs7243248	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7244723	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73410960	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7506731	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8082868	0.80[EUR][1000 genomes]
rs8082888	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8083240	0.82[EUR][1000 genomes]
rs8087637	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8089305	0.83[ASN][1000 genomes]
rs8091463	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8091585	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8093417	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8095234	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8095647	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8099334	0.83[EUR][1000 genomes]
rs8099792	0.81[EUR][1000 genomes]
rs9303759	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9303760	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs948752	0.82[EUR][1000 genomes]
rs949229	0.83[EUR][1000 genomes]
rs949230	0.83[EUR][1000 genomes]
rs949232	0.83[EUR][1000 genomes]
rs949233	0.82[EUR][1000 genomes]
rs9945491	0.85[AMR][1000 genomes]
rs9948384	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9949350	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9951744	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9951822	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9951904	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9951929	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9952038	0.83[EUR][1000 genomes]
rs9953892	0.81[AMR][1000 genomes]
rs9954852	0.86[AMR][1000 genomes]
rs9954861	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9954884	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9955629	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9956465	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9956997	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9957303	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9959517	0.82[EUR][1000 genomes]
rs9959561	0.83[EUR][1000 genomes]
rs9959641	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9959774	0.83[EUR][1000 genomes]
rs9959781	0.83[EUR][1000 genomes]
rs9960429	0.83[EUR][1000 genomes]
rs9960443	0.82[EUR][1000 genomes]
rs9963587	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9964971	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9965004	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9965108	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9966458	0.91[AFR][1000 genomes]
rs9966965	0.84[AMR][1000 genomes]
rs9967372	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
4	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
13	nsv961151	chr18:12082154-12099861	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv909398	chr18:12083552-12121294	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv909399	chr18:12083552-12141372	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1815925	RP11-64C12.3	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12077000-12095000	Weak transcription	Right Atrium	heart
2	chr18:12089000-12093800	Weak transcription	Spleen	Spleen
3	chr18:12091200-12094000	Enhancers	Esophagus	oesophagus
4	chr18:12093000-12094200	Enhancers	Placenta	Placenta
5	chr18:12093200-12093800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:12093200-12093800	Weak transcription	Pancreas	Pancrea

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