Variant report

Variant	rs11669558
Chromosome Location	chr19:19655670-19655671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19653642..19665886-chr19:19736282..19742268,24	MCF-7	breast:
2	chr19:19654766..19656618-chr19:19752762..19755069,2	MCF-7	breast:
3	chr19:19630106..19632740-chr19:19655430..19658007,2	K562	blood:
4	chr19:19655485..19657839-chr19:19672658..19674603,2	K562	blood:

Variant related genes	Relation type
ENSG00000064547	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1036215	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10406278	0.81[EUR][1000 genomes]
rs11085264	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11668203	0.86[EUR][1000 genomes]
rs11669730	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670687	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11670761	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670775	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670882	0.92[EUR][1000 genomes]
rs11671253	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1560687	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16996127	0.96[EUR][1000 genomes]
rs17684164	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2060274	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2060275	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916070	0.84[EUR][1000 genomes]
rs2916072	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2916075	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965179	0.84[EUR][1000 genomes]
rs2965181	0.84[EUR][1000 genomes]
rs2965184	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34487417	0.82[EUR][1000 genomes]
rs34667451	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs45556231	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs45631651	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4808204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4808205	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808206	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808951	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4808958	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4808962	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4808968	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808969	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4808970	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55927782	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56280531	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56291054	0.82[EUR][1000 genomes]
rs56330647	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58074958	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61744761	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245689	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7250233	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7252453	0.93[EUR][1000 genomes]
rs7256028	0.96[EUR][1000 genomes]
rs751857	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754256	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8100927	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8101219	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8102502	0.91[EUR][1000 genomes]
rs8105642	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8110171	0.85[EUR][1000 genomes]
rs8110250	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv543928	chr19:19649839-19664043	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11669558	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19652000-19688400	Weak transcription	Right Atrium	heart
3	chr19:19652200-19657600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:19652200-19658000	Weak transcription	Right Ventricle	heart
5	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:19652600-19659000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr19:19652600-19660800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:19652600-19686200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:19652800-19657000	Weak transcription	Fetal Heart	heart
10	chr19:19653800-19657200	Weak transcription	Hela-S3	cervix
11	chr19:19654000-19656400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:19654800-19656200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:19655200-19656400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:19655400-19659200	Bivalent Enhancer	Placenta	Placenta
15	chr19:19655600-19656000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:19655600-19656200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:19655600-19660800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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