Variant report

Variant	rs35679807
Chromosome Location	chr15:41853106-41853107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41852819-41853144	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr15:41853080-41853230	BE2_C	brain:	n/a	n/a
3	ZNF263	chr15:41851058-41853318	HEK293-T-REx	kidney:	n/a	chr15:41851388-41851409 chr15:41851348-41851369 chr15:41851896-41851905 chr15:41851160-41851169

No.	Distal block	Cell Line	Cell type
1	chr15:41851361..41854178-chr15:42065182..42067599,2	K562	blood:
2	chr15:41853024..41855719-chr15:41894877..41896959,2	K562	blood:
3	chr15:41851029..41853126-chr15:41899971..41902269,2	K562	blood:
4	chr15:41779821..41781548-chr15:41852797..41854697,2	MCF-7	breast:
5	chr15:41847317..41853712-chr15:41951201..41955578,8	K562	blood:
6	chr15:41835713..41840265-chr15:41851401..41853463,4	K562	blood:
7	chr15:41849459..41853162-chr15:41854225..41857161,4	MCF-7	breast:
8	chr15:41784400..41789772-chr15:41847283..41854059,7	K562	blood:
9	chr15:41850576..41853126-chr15:41900769..41903357,2	K562	blood:

Variant related genes	Relation type
TYRO3	TF binding region
ENSG00000103932	Chromatin interaction
ENSG00000092445	Chromatin interaction
ENSG00000137825	Chromatin interaction
ENSG00000137802	Chromatin interaction
ENSG00000174197	Chromatin interaction
ENSG00000260926	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1023194	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1200341	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16971872	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8040005	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3311131	chr15:41851466-41853360	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	esv3311132	chr15:41851466-41853360	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35679807	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41850200-41853200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:41851800-41853200	Flanking Active TSS	Dnd41	blood
3	chr15:41852000-41853200	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:41852000-41853400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:41852000-41853400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:41852000-41853400	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr15:41852000-41853800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:41852200-41853200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr15:41852200-41853200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:41852200-41853200	Flanking Active TSS	Fetal Brain Female	brain
11	chr15:41852200-41854000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr15:41852200-41854400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:41852200-41854400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
15	chr15:41852400-41853200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:41852400-41853200	Enhancers	Gastric	stomach
17	chr15:41852400-41853400	Enhancers	Right Ventricle	heart
18	chr15:41852400-41853400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
19	chr15:41852400-41853600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:41852400-41853600	Enhancers	Pancreas	Pancrea
21	chr15:41852400-41853800	Weak transcription	A549	lung
22	chr15:41852400-41854200	Enhancers	Right Atrium	heart
23	chr15:41852400-41854200	Weak transcription	HSMMtube	muscle
24	chr15:41852400-41854200	Weak transcription	Osteobl	bone
25	chr15:41852400-41854400	Enhancers	Placenta	Placenta
26	chr15:41852400-41854600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:41852400-41854800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:41852400-41855200	Weak transcription	HSMM	muscle
29	chr15:41852400-41859600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
31	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:41852600-41853200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41852600-41853200	Enhancers	NH-A	brain
34	chr15:41852600-41853400	Enhancers	H9 Cell Line	embryonic stem cell
35	chr15:41852600-41853400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:41852600-41853400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:41852600-41853400	Enhancers	Stomach Mucosa	stomach
38	chr15:41852600-41853600	Flanking Active TSS	Brain Angular Gyrus	brain
39	chr15:41852600-41853600	Enhancers	Duodenum Mucosa	Duodenum
40	chr15:41852600-41853800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:41852600-41853800	Enhancers	K562	blood
42	chr15:41852600-41854000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr15:41852600-41854200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:41852600-41854200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:41852600-41854200	Enhancers	Fetal Brain Male	brain
46	chr15:41852600-41855000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:41852600-41855000	Enhancers	Fetal Lung	lung
48	chr15:41852600-41855400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:41852600-41855400	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr15:41852600-41856800	Enhancers	HepG2	liver

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