Variant report

Variant	rs1326120
Chromosome Location	chr13:50729244-50729245
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	chr13:50727152..50729552-chr13:50729761..50732291,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2066549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2066557	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2066558	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2066572	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2066575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2066585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2066587	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2066591	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066594	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2687950	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2687951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2740508	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2740524	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2740544	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2740545	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2760914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2803839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs2812204	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812216	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2812217	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2812222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2997624	0.82[AMR][1000 genomes]
rs4942901	0.91[AMR][1000 genomes]
rs790943	0.90[CHB][hapmap]
rs9568363	0.88[AMR][1000 genomes]
rs9568364	0.88[AMR][1000 genomes]
rs9568366	0.94[CHB][hapmap]
rs9596215	0.86[AMR][1000 genomes]
rs9596219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs9596220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	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
rs1326120	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs1326120	DLEU2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50724400-50729400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:50724400-50730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:50724400-50730400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:50724400-50733400	Weak transcription	Psoas Muscle	Psoas
5	chr13:50726800-50730000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:50726800-50734600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:50726800-50735000	Weak transcription	NHLF	lung
8	chr13:50727000-50730200	Weak transcription	NHDF-Ad	bronchial
9	chr13:50727000-50730600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:50727000-50730600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:50727000-50732400	Weak transcription	Primary B cells from cord blood	blood
12	chr13:50727400-50729800	Weak transcription	HepG2	liver
13	chr13:50727600-50730200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr13:50727800-50730200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:50727800-50730600	Weak transcription	HSMM	muscle
16	chr13:50728000-50730000	Weak transcription	Osteobl	bone
17	chr13:50728000-50732600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr13:50728200-50730000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:50728200-50730400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:50728200-50731200	Enhancers	Dnd41	blood
21	chr13:50728800-50733400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:50729000-50731800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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