Variant report

Variant	rs400011
Chromosome Location	chr19:39568654-39568655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39565899..39568671-chr3:161088109..161090760,2	MCF-7	breast:
2	chr19:39526693..39529184-chr19:39566725..39569356,2	K562	blood:
3	chr19:39566476..39569362-chr19:39573517..39575848,2	K562	blood:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000183760	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10407957	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10408661	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12151180	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2569365	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34738600	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs377373	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs380679	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs384605	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs385681	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392005	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs392135	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs393559	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs395387	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs396616	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs397189	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs420682	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs426076	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs452666	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs453853	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802015	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803196	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803197	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs482679	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487456	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs578940	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs597995	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs602744	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs609327	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs620642	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs621580	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs648192	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs648635	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs665998	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs690812	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs691059	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs691114	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs691256	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs691266	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs691391	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs691890	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs692294	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs692343	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs774727	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs774927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs774928	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv522530	chr19:39552150-39573918	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1067028	chr19:39567228-39622846	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1060469	chr19:39567228-39624790	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 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	chr19:39562000-39570000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:39564600-39569200	Weak transcription	Brain Hippocampus Middle	brain
3	chr19:39564600-39569600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:39564600-39569600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:39565000-39571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:39565200-39568800	Weak transcription	Osteobl	bone
7	chr19:39565200-39569000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr19:39565200-39569000	Weak transcription	Hela-S3	cervix
9	chr19:39565400-39573000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:39565400-39573200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:39565800-39569000	Weak transcription	HUVEC	blood vessel
12	chr19:39566000-39569000	Weak transcription	NH-A	brain
13	chr19:39567400-39574000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr19:39567800-39569200	Enhancers	A549	lung
15	chr19:39568000-39570800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:39568200-39569400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:39568400-39570000	Enhancers	NHDF-Ad	bronchial
18	chr19:39568400-39570000	Enhancers	NHEK	skin
19	chr19:39568400-39570200	Enhancers	Brain Anterior Caudate	brain
20	chr19:39568400-39570600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:39568400-39571600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:39568600-39570200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:39568600-39570200	Enhancers	HMEC	breast

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