Variant report

Variant	rs10752940
Chromosome Location	chr1:184630291-184630292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:184610419..184613412-chr1:184629459..184632397,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10911631	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10911644	0.91[CEU][hapmap]
rs10911645	0.84[CEU][hapmap]
rs12124929	0.87[CEU][hapmap]
rs12131285	0.96[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12137438	0.85[EUR][1000 genomes]
rs12567225	0.91[CEU][hapmap]
rs12567226	0.91[CEU][hapmap]
rs2064605	0.92[CEU][hapmap]
rs2333715	0.91[CEU][hapmap]
rs2877994	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4233120	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4651230	0.91[CEU][hapmap]
rs6662416	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9425338	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9425340	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9425343	0.91[CEU][hapmap]
rs9425632	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv947339	chr1:184618714-184641256	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10752940	EDEM3	cis	Esophagus Muscularis	GTEx
rs10752940	EDEM3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184625400-184633000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:184625800-184631000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:184625800-184632800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:184626400-184632600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr1:184626600-184632600	Weak transcription	Brain Substantia Nigra	brain
6	chr1:184626600-184632800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:184626800-184632800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:184626800-184633000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:184627400-184632600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:184628800-184630400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:184629400-184631800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:184629600-184630600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:184629600-184630800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:184629800-184631000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:184629800-184631000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:184629800-184631000	Weak transcription	A549	lung
17	chr1:184629800-184631600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:184629800-184633000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:184629800-184633000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:184630000-184630800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:184630000-184631600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr1:184630000-184633000	Weak transcription	Ovary	ovary
23	chr1:184630200-184631800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:184630200-184632800	Weak transcription	Spleen	Spleen

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