Variant report

Variant	rs10409615
Chromosome Location	chr19:53568151-53568152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53565063..53566659-chr19:53568054..53569781,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10406237	1.00[ASN][1000 genomes]
rs10410030	1.00[ASN][1000 genomes]
rs10412805	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418505	1.00[ASN][1000 genomes]
rs16984438	1.00[ASN][1000 genomes]
rs16984443	1.00[ASN][1000 genomes]
rs16984486	1.00[ASN][1000 genomes]
rs28368410	1.00[ASN][1000 genomes]
rs28528321	1.00[ASN][1000 genomes]
rs28661145	1.00[ASN][1000 genomes]
rs28662846	1.00[ASN][1000 genomes]
rs28691095	1.00[ASN][1000 genomes]
rs28701520	1.00[ASN][1000 genomes]
rs28726276	1.00[ASN][1000 genomes]
rs58143828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509725	1.00[ASN][1000 genomes]
rs7247568	1.00[ASN][1000 genomes]
rs7253566	1.00[ASN][1000 genomes]
rs73935216	1.00[ASN][1000 genomes]
rs73935236	1.00[ASN][1000 genomes]
rs8099848	1.00[ASN][1000 genomes]
rs8100134	1.00[ASN][1000 genomes]
rs8102799	1.00[ASN][1000 genomes]
rs8113824	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	esv1800937	chr19:53514613-53573309	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1834009	chr19:53518514-53569196	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1056648	chr19:53518514-53569196	Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1055423	chr19:53524199-53569196	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10409615	LMO2	trans	lymphoblastoid	seeQTL
rs10409615	C10orf99	trans	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53559600-53568200	Weak transcription	Dnd41	blood
2	chr19:53561800-53569400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr19:53562200-53570400	Weak transcription	HSMMtube	muscle
4	chr19:53562400-53568400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:53562800-53569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:53563400-53568600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr19:53564400-53577000	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:53564600-53586800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:53564800-53586600	ZNF genes & repeats	Liver	Liver
10	chr19:53565000-53569600	ZNF genes & repeats	Aorta	Aorta
11	chr19:53565600-53569000	Weak transcription	Brain Anterior Caudate	brain
12	chr19:53565600-53570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:53566000-53574400	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:53566200-53573600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
15	chr19:53566200-53577400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:53566400-53568600	ZNF genes & repeats	Brain Germinal Matrix	brain
17	chr19:53566600-53575400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:53566800-53570400	Weak transcription	Fetal Kidney	kidney
19	chr19:53566800-53570600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr19:53567000-53568400	Weak transcription	Ovary	ovary
21	chr19:53567000-53569400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:53567000-53570000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:53567000-53574200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:53567400-53568600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:53567400-53568600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:53567800-53576800	ZNF genes & repeats	Fetal Muscle Leg	muscle
27	chr19:53568000-53569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:53568000-53569400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:53568000-53580600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:53568000-53586400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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