Variant report

Variant	rs17559081
Chromosome Location	chr3:138831185-138831186
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138830591..138831327-chr3:138920891..138921850,5	MCF-7	breast:
2	chr3:138830444..138831348-chr3:138920931..138921772,3	K562	blood:
3	chr3:138830004..138832870-chr3:139047929..139048811,16	MCF-7	breast:
4	chr3:138830340..138831523-chr3:139047812..139048878,10	K562	blood:
5	chr3:138830459..138831302-chr3:138920846..138921696,3	MCF-7	breast:
6	chr3:138830341..138831717-chr3:139047849..139048818,6	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10513056	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12493424	1.00[CEU][hapmap]
rs12632179	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap]
rs17486826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688683	1.00[MKK][hapmap];0.83[TSI][hapmap]
rs2737734	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap]
rs57102621	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs581530	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs584059	1.00[CEU][hapmap]
rs586043	1.00[CEU][hapmap]
rs599157	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs60339757	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60884457	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs633876	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs649829	1.00[CEU][hapmap]
rs663729	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs676102	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs73864935	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73864936	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73866277	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv829736	chr3:138737352-138934758	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138820600-138839000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:138827400-138831200	Enhancers	Liver	Liver
3	chr3:138830600-138831200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:138830600-138831200	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:138830600-138831200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
6	chr3:138830600-138831200	Enhancers	NHDF-Ad	bronchial
7	chr3:138830600-138831400	Enhancers	Brain Angular Gyrus	brain
8	chr3:138830600-138831400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr3:138830800-138831200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:138830800-138831200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:138830800-138831200	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:138830800-138831200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr3:138830800-138831200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:138830800-138831200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:138830800-138831200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
16	chr3:138830800-138831200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:138830800-138831200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:138830800-138831200	Enhancers	Brain Anterior Caudate	brain
19	chr3:138830800-138831200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr3:138830800-138831200	Enhancers	Ovary	ovary
21	chr3:138830800-138831200	Enhancers	Pancreas	Pancrea
22	chr3:138830800-138831200	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:138830800-138831400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:138830800-138833000	Enhancers	Brain Hippocampus Middle	brain
25	chr3:138831000-138831200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:138831000-138831200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:138831000-138831200	Enhancers	Adipose Nuclei	Adipose
28	chr3:138831000-138831200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr3:138831000-138831200	Bivalent Enhancer	Fetal Stomach	stomach
30	chr3:138831000-138831200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr3:138831000-138831200	Enhancers	Spleen	Spleen
32	chr3:138831000-138831400	Enhancers	K562	blood
33	chr3:138831000-138836000	Weak transcription	HSMM	muscle

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