Variant report

Variant	rs12359896
Chromosome Location	chr10:5189503-5189504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5189042..5190566-chr10:5324451..5326870,2	MCF-7	breast:
2	chr10:5166174..5167900-chr10:5189108..5191670,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10508294	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10904415	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10904416	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10904436	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10904439	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11252931	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11252934	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11252935	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11252936	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11252937	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11252941	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11252955	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11252968	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252972	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11252978	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11252992	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11253008	0.85[AMR][1000 genomes]
rs11253010	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11253012	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11253013	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11253015	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11253019	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11253020	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11253021	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11253022	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11253036	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11253039	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11492955	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11517338	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11517343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11517344	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12354416	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12354530	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12357445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12357449	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12360480	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12769156	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1334466	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1334467	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1334471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1334738	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1334739	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17134288	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17305952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1889458	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1937843	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1937909	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2020172	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2210679	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2895061	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2895064	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34914591	0.89[AMR][1000 genomes]
rs35219485	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3763676	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4448597	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4880711	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4880714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4880715	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4881406	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4881407	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6601907	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6601918	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7069331	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7090349	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7090531	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7097295	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7097646	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7477623	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7478099	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7741	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7920141	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7920454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9730736	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9794203	0.95[AMR][1000 genomes];0.96[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	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	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5188800-5189800	Enhancers	Liver	Liver
2	chr10:5188800-5191200	Enhancers	Fetal Intestine Small	intestine
3	chr10:5189000-5189800	Enhancers	Duodenum Mucosa	Duodenum
4	chr10:5189000-5189800	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr10:5189000-5191200	Enhancers	Fetal Intestine Large	intestine
6	chr10:5189200-5189600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr10:5189200-5189600	Flanking Active TSS	HepG2	liver
8	chr10:5189200-5190200	Enhancers	Colonic Mucosa	Colon
9	chr10:5189200-5190400	Enhancers	Small Intestine	intestine
10	chr10:5189200-5190400	Enhancers	Stomach Mucosa	stomach
11	chr10:5189200-5190600	Enhancers	Pancreas	Pancrea
12	chr10:5189200-5190600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr10:5189200-5191800	Flanking Active TSS	A549	lung
14	chr10:5189400-5191800	Enhancers	Hela-S3	cervix

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