Variant report

Variant	rs56395748
Chromosome Location	chr5:96176893-96176894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96142480..96144283-chr5:96175834..96178694,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10515246	1.00[AFR][1000 genomes]
rs10515247	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10515248	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10515249	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10515250	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11135480	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11738115	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11738810	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11739020	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11740375	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11740598	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11741100	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11742261	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743410	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11746534	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11747148	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11747179	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11747896	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11748328	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11748519	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11748795	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749811	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11750464	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11750671	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11750934	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12186366	1.00[AFR][1000 genomes]
rs13601	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs17401901	1.00[AFR][1000 genomes]
rs17402639	1.00[AFR][1000 genomes]
rs17402704	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17405676	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17481334	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17481759	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17481856	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17484359	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2042386	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3333	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3334	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3335	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35898772	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55773007	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs55996659	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56119802	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56213813	0.81[EUR][1000 genomes]
rs56319744	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72773905	1.00[AFR][1000 genomes]
rs72773906	1.00[AFR][1000 genomes]
rs72773912	1.00[AFR][1000 genomes]
rs72773917	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs72773922	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72773923	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72773932	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72773942	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72773947	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72773950	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs72773968	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs72773969	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72773981	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72773986	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72773989	0.98[EUR][1000 genomes]
rs72773991	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72775807	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72775809	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72775817	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs72775818	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96172000-96179200	Weak transcription	Fetal Thymus	thymus
2	chr5:96172200-96180400	Weak transcription	Thymus	Thymus
3	chr5:96172400-96178800	Weak transcription	Dnd41	blood
4	chr5:96173400-96177000	Enhancers	Fetal Intestine Large	intestine
5	chr5:96174000-96177400	Enhancers	Fetal Intestine Small	intestine
6	chr5:96175200-96179800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:96175200-96180000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:96175400-96179800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:96175400-96180000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:96175600-96178800	Weak transcription	NHEK	skin
11	chr5:96175800-96180200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:96176000-96177000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:96176800-96177000	Enhancers	Placenta	Placenta
14	chr5:96176800-96177000	Enhancers	GM12878-XiMat	blood
15	chr5:96176800-96177200	Enhancers	Psoas Muscle	Psoas
16	chr5:96176800-96177400	Enhancers	Fetal Heart	heart

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