Variant report

Variant	rs17216525
Chromosome Location	chr19:19662220-19662221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19662094..19664992-chr19:19773250..19775543,2	MCF-7	breast:
2	chr19:19661215..19662873-chr19:19705870..19708009,2	MCF-7	breast:
3	chr19:19661739..19664065-chr19:19676353..19678590,2	MCF-7	breast:
4	chr19:19650632..19654238-chr19:19660662..19664611,5	K562	blood:
5	chr19:19653642..19665886-chr19:19736282..19742268,24	MCF-7	breast:
6	chr19:19660178..19662457-chr19:19724414..19727027,3	MCF-7	breast:
7	chr19:19659913..19662328-chr19:19729922..19731592,2	MCF-7	breast:
8	chr19:19658728..19665195-chr19:19751348..19756166,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160161	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10415849	0.83[JPT][hapmap]
rs10500212	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11668386	1.00[YRI][hapmap]
rs12608729	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12610185	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12610191	0.84[EUR][1000 genomes]
rs16996148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16996185	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs17216588	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794991	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56255430	0.89[AMR][1000 genomes]
rs57504626	0.84[EUR][1000 genomes]
rs58847337	0.84[EUR][1000 genomes]
rs73002956	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73004926	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73004933	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73004951	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73004959	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73004962	0.84[EUR][1000 genomes]
rs73004966	0.82[EUR][1000 genomes]
rs73004975	0.82[EUR][1000 genomes]
rs8182472	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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

Variant related diseases (count:1)

Disease	PMID	Source
Triglycerides	19060906	GWAS catalog

Chromatin state (count:22 , 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	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:19652600-19686200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:19659200-19663600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:19659200-19686200	Weak transcription	Fetal Brain Male	brain
7	chr19:19660600-19663000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:19660600-19663600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:19660800-19663800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr19:19661000-19662800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:19661000-19663600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:19661200-19670800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:19661400-19675600	Weak transcription	Ovary	ovary
14	chr19:19661400-19677800	Weak transcription	Fetal Lung	lung
15	chr19:19661600-19662600	Weak transcription	Osteobl	bone
16	chr19:19661600-19663400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:19661600-19673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:19661800-19662600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:19661800-19673400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:19662000-19662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:19662200-19663200	Enhancers	Fetal Muscle Leg	muscle
22	chr19:19662200-19663600	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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