Variant report

Variant	rs12354530
Chromosome Location	chr10:5131305-5131306
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	TCF12	chr10:5130891-5131482	A549	lung:	n/a	n/a
2	SETDB1	chr10:5130881-5131647	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5118918..5120947-chr10:5130785..5133580,2	MCF-7	breast:

Variant related genes	Relation type
AKR1C3	TF binding region
ENSG00000196139	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10508294	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10904415	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10904416	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10904436	0.84[AMR][1000 genomes]
rs10904439	0.81[AMR][1000 genomes]
rs11252928	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11252931	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11252934	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11252935	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11252936	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11252937	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11252941	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11252955	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11252968	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11252972	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11252978	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11252992	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11253010	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11253012	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11253013	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11253015	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11253016	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11253018	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11253019	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11253020	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11253021	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11253022	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11253036	0.82[AMR][1000 genomes]
rs11253039	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11492955	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11517338	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11517343	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11517344	0.88[AMR][1000 genomes]
rs12354416	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12357445	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12357449	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12359896	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12360480	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12769156	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1334466	0.82[AMR][1000 genomes]
rs1334467	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1334471	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1334738	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1334739	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17134288	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17305952	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1889458	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1937843	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1937909	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2020172	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2210679	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2398200	0.83[GIH][hapmap]
rs2895061	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2895064	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34914591	0.83[AMR][1000 genomes]
rs35219485	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3763676	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4448597	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4880711	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes]
rs4880714	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4880715	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4881406	0.96[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4881407	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6601901	0.86[EUR][1000 genomes]
rs6601907	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6601918	0.85[AMR][1000 genomes]
rs7069331	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7090349	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7090531	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7097295	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7097646	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7477623	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7478099	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7920141	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7920454	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9730736	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9794203	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv948794	chr10:4863093-5227382	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1045155	chr10:4872239-5211318	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040343	chr10:4872814-5196815	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540462	chr10:4872814-5196815	Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv869470	chr10:4878904-5203685	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv1050246	chr10:4927428-5211318	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv549882	chr10:4943518-5203864	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	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
13	nsv430122	chr10:4986040-5134511	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	nsv1036667	chr10:5076258-5133621	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	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
19	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
20	nsv1042487	chr10:5090313-5196900	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv540463	chr10:5090313-5196900	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv540464	chr10:5108345-5196815	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	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
24	nsv540466	chr10:5114577-5196815	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	nsv540467	chr10:5114577-5225365	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	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
27	nsv540469	chr10:5120774-5225365	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12354530	AKR1C3	cis	cerebellum	SCAN
rs12354530	AKR1C3	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5122000-5132200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:5129800-5131800	ZNF genes & repeats	A549	lung
3	chr10:5131000-5132000	Weak transcription	Duodenum Mucosa	Duodenum

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