Variant report

Variant	rs11249799
Chromosome Location	chr5:177792487-177792488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:177777429..177779459-chr5:177792254..177794069,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253698	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11249800	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11249801	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11746402	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519834	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17081159	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17580670	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2910120	0.87[ASN][1000 genomes]
rs2973721	0.87[ASN][1000 genomes]
rs2973722	0.87[ASN][1000 genomes]
rs2973723	0.87[ASN][1000 genomes]
rs2973725	0.87[ASN][1000 genomes]
rs4293937	0.88[ASN][1000 genomes]
rs72820973	0.88[EUR][1000 genomes]
rs72820974	0.89[EUR][1000 genomes]
rs72820976	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72822841	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72822842	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72822844	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
5	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv883206	chr5:177684682-177796121	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1027165	chr5:177693601-177843314	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS 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	6 gene(s)	inside rSNPs	diseases
11	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv883211	chr5:177787515-177820134	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv462569	chr5:177787515-177821665	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv600398	chr5:177787515-177821665	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv883212	chr5:177790952-177820134	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177784400-177796800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:177784400-177798200	Weak transcription	Right Atrium	heart
3	chr5:177785200-177798200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:177787200-177798200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:177789200-177795800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:177789400-177792800	Weak transcription	Thymus	Thymus
7	chr5:177790200-177792600	Enhancers	Fetal Thymus	thymus
8	chr5:177790600-177793400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr5:177790800-177794200	Enhancers	Placenta	Placenta
10	chr5:177791200-177793200	Bivalent Enhancer	Fetal Stomach	stomach
11	chr5:177791200-177795000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:177791400-177792600	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr5:177791600-177793000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr5:177791600-177794600	Weak transcription	Spleen	Spleen
15	chr5:177791800-177793000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr5:177792000-177793400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr5:177792000-177794000	Weak transcription	Fetal Lung	lung
18	chr5:177792000-177794600	Weak transcription	Dnd41	blood
19	chr5:177792200-177792800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr5:177792200-177795400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr5:177792400-177793000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:177792400-177795600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:177792400-177796000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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