Variant report

Variant	rs4880716
Chromosome Location	chr10:5238196-5238197
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	RAD21	chr10:5237878-5238218	HepG2	liver:	n/a	n/a
2	CEBPB	chr10:5237938-5238377	A549	lung:	n/a	n/a
3	MAX	chr10:5237558-5238405	A549	lung:	n/a	n/a
4	TCF7L2	chr10:5237966-5238641	HepG2	liver:	n/a	chr10:5238174-5238183 chr10:5238175-5238182 chr10:5238175-5238185 chr10:5238172-5238186
5	EP300	chr10:5237490-5238515	A549	lung:	n/a	chr10:5238159-5238173 chr10:5238166-5238180
6	CEBPB	chr10:5238003-5238282	HepG2	liver:	n/a	n/a
7	BCL3	chr10:5237721-5238466	A549	lung:	n/a	n/a
8	CEBPB	chr10:5237933-5238462	A549	lung:	n/a	n/a
9	SMC3	chr10:5237784-5238429	HepG2	liver:	n/a	n/a
10	E2F6	chr10:5237704-5238198	A549	lung:	n/a	n/a
11	MYBL2	chr10:5237782-5238428	HepG2	liver:	n/a	n/a
12	CEBPB	chr10:5237719-5238565	A549	lung:	n/a	n/a
13	FOXA2	chr10:5237844-5238456	A549	lung:	n/a	n/a
14	FOXA1	chr10:5238047-5238284	HepG2	liver:	n/a	n/a
15	TCF12	chr10:5237533-5239259	A549	lung:	n/a	n/a
16	EP300	chr10:5237845-5238408	HepG2	liver:	n/a	chr10:5238159-5238173 chr10:5238166-5238180
17	HNF4G	chr10:5237969-5238290	HepG2	liver:	n/a	chr10:5238103-5238115 chr10:5238102-5238115 chr10:5238102-5238115 chr10:5238102-5238117 chr10:5238102-5238117 chr10:5238103-5238116 chr10:5238102-5238117 chr10:5238100-5238115 chr10:5238108-5238116 chr10:5238102-5238116 chr10:5238103-5238115
18	SP1	chr10:5237874-5238382	HepG2	liver:	n/a	n/a
19	GATA3	chr10:5237438-5238563	A549	lung:	n/a	n/a
20	REST	chr10:5237770-5238431	A549	lung:	n/a	n/a
21	FOSL2	chr10:5237618-5238464	A549	lung:	n/a	n/a
22	ARID3A	chr10:5237741-5238762	HepG2	liver:	n/a	n/a
23	FOXA2	chr10:5237961-5238266	HepG2	liver:	n/a	n/a
24	FOXA1	chr10:5237758-5238382	HepG2	liver:	n/a	n/a
25	FOXA1	chr10:5237854-5238293	HepG2	liver:	n/a	n/a
26	FOXA2	chr10:5237810-5238481	HepG2	liver:	n/a	n/a
27	SP1	chr10:5237463-5239164	A549	lung:	n/a	n/a
28	HNF4A	chr10:5237973-5238295	HepG2	liver:	n/a	chr10:5238103-5238115 chr10:5238102-5238115 chr10:5238102-5238115 chr10:5238102-5238117 chr10:5238102-5238117 chr10:5238103-5238116 chr10:5238102-5238117 chr10:5238108-5238116 chr10:5238102-5238116 chr10:5238101-5238116 chr10:5238103-5238115
29	CEBPB	chr10:5237947-5238365	HepG2	liver:	n/a	n/a
30	EP300	chr10:5237924-5238372	HepG2	liver:	n/a	chr10:5238159-5238173 chr10:5238166-5238180
31	HNF4A	chr10:5237926-5238244	HepG2	liver:	n/a	chr10:5238103-5238115 chr10:5238102-5238115 chr10:5238102-5238115 chr10:5238102-5238117 chr10:5238102-5238117 chr10:5238103-5238116 chr10:5238102-5238117 chr10:5238108-5238116 chr10:5238102-5238116 chr10:5238101-5238116 chr10:5238103-5238115
32	SP1	chr10:5237526-5238474	A549	lung:	n/a	n/a
33	NFIC	chr10:5237673-5238378	HepG2	liver:	n/a	n/a
34	MAX	chr10:5237664-5238367	A549	lung:	n/a	n/a
35	EP300	chr10:5237568-5238515	A549	lung:	n/a	chr10:5238159-5238173 chr10:5238166-5238180

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1C4-2	chr10:5238192-5238885	NONHSAT011140

Variant related genes	Relation type
ENSG00000251909	TF binding region
AKR1C4	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11253038	0.84[CHB][hapmap]
rs11594428	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11594448	1.00[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11596429	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12360316	0.84[CHB][hapmap]
rs17134523	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17306779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895055	0.84[CHB][hapmap]
rs3812616	0.90[ASN][1000 genomes]
rs3812617	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4612705	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4880713	0.84[CHB][hapmap]
rs61854738	0.90[ASN][1000 genomes]
rs61854739	0.90[ASN][1000 genomes]
rs7070862	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs7074004	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7085249	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7087111	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7088788	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7091223	0.84[CHB][hapmap]
rs7100517	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72772224	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72772226	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894792	chr10:4832920-5498724	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv466713	chr10:4901798-5319679	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription 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
3	nsv549881	chr10:4901798-5319679	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	esv2763913	chr10:4961021-5321407	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1039386	chr10:5008383-5348491	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1036566	chr10:5037926-5261426	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv549883	chr10:5037926-5275762	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1047484	chr10:5076258-5261482	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1036291	chr10:5076258-5456234	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv540465	chr10:5108345-5261482	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv540468	chr10:5114577-5261482	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
13	nsv540470	chr10:5120774-5261482	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv540471	chr10:5133561-5261482	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv540472	chr10:5133561-5284334	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1048081	chr10:5149144-5321395	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	esv3387745	chr10:5201939-5324885	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv3370619	chr10:5201974-5324834	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	esv3320807	chr10:5202006-5324760	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	esv3521675	chr10:5202012-5324815	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv3521676	chr10:5202012-5324815	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	esv3332233	chr10:5202023-5324788	ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
23	esv3405253	chr10:5202043-5324758	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	esv4943	chr10:5202052-5324829	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
25	esv3320818	chr10:5202105-5324796	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
26	nsv932104	chr10:5203626-5641023	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
27	nsv549886	chr10:5205437-5632060	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
28	nsv1054865	chr10:5225305-5638119	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
29	nsv5643	chr10:5229780-5302665	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4880716	AKR1C3	cis	brain	seeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5235600-5239600	Enhancers	HepG2	liver
2	chr10:5236600-5238800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:5237000-5239800	Enhancers	Stomach Mucosa	stomach
4	chr10:5237600-5239400	Enhancers	Fetal Intestine Large	intestine
5	chr10:5237600-5239400	Enhancers	Fetal Intestine Small	intestine
6	chr10:5237800-5238200	Active TSS	Liver	Liver
7	chr10:5237800-5238400	Active TSS	A549	lung
8	chr10:5238000-5238400	Weak transcription	Pancreas	Pancrea

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