Variant report

Variant	rs6580732
Chromosome Location	chr12:50646279-50646280
allele	G/T
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	GATA3	chr12:50645500-50646818	MCF-7	breast:	n/a	chr12:50646566-50646574 chr12:50646567-50646574 chr12:50645940-50645947 chr12:50646567-50646574 chr12:50645929-50645939 chr12:50646567-50646574

No.	Distal block	Cell Line	Cell type
1	chr12:50645859..50648042-chr12:50675883..50677407,2	MCF-7	breast:
2	chr12:50632639..50636668-chr12:50645758..50650000,5	MCF-7	breast:
3	chr12:50643519..50647012-chr12:50649051..50651928,4	K562	blood:
4	chr12:50645486..50647003-chr12:50676682..50678862,2	MCF-7	breast:
5	chr12:50610860..50612440-chr12:50643733..50646467,2	MCF-7	breast:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000212496	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000257531	Chromatin interaction
ENSG00000203433	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10219559	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783342	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10783343	0.87[AMR][1000 genomes]
rs1362984	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1862042	0.84[AMR][1000 genomes]
rs2004283	0.89[AMR][1000 genomes]
rs4459386	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6580734	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7136648	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301566	0.82[EUR][1000 genomes]
rs7308692	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7309519	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7957659	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7967954	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8181679	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9668955	0.85[AMR][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	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6580732	CERS5	cis	Nerve Tibial	GTEx
rs6580732	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50616800-50651800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:50633200-50651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:50634600-50648200	Weak transcription	Spleen	Spleen
4	chr12:50635600-50646600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:50636200-50651200	Weak transcription	Fetal Kidney	kidney
6	chr12:50636600-50651400	Weak transcription	Gastric	stomach
7	chr12:50636600-50651800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:50636800-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:50637200-50648200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:50639000-50651600	Weak transcription	Fetal Lung	lung
11	chr12:50640400-50651200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:50640800-50647400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
14	chr12:50641200-50653200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:50641400-50647800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
17	chr12:50641800-50648400	Weak transcription	Lung	lung
18	chr12:50641800-50651200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:50641800-50651200	Weak transcription	Left Ventricle	heart
20	chr12:50641800-50651200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:50641800-50651800	Weak transcription	Fetal Stomach	stomach
22	chr12:50641800-50651800	Weak transcription	Right Ventricle	heart
23	chr12:50641800-50652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:50642600-50651200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:50642600-50652000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:50642800-50649000	Weak transcription	Aorta	Aorta
27	chr12:50642800-50651200	Weak transcription	Brain Angular Gyrus	brain
28	chr12:50643000-50647400	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr12:50643000-50648600	Weak transcription	Pancreas	Pancrea
30	chr12:50643000-50649400	Enhancers	Fetal Intestine Large	intestine
31	chr12:50643000-50651000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:50643000-50651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:50643200-50651000	Weak transcription	Adipose Nuclei	Adipose
34	chr12:50643400-50648000	Weak transcription	NHDF-Ad	bronchial
35	chr12:50643600-50648000	Weak transcription	NH-A	brain
36	chr12:50643600-50649200	Enhancers	Stomach Mucosa	stomach
37	chr12:50643800-50646800	Weak transcription	A549	lung
38	chr12:50643800-50651000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:50643800-50651200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:50643800-50651400	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:50644000-50647400	Weak transcription	Hela-S3	cervix
42	chr12:50644000-50647800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:50644000-50651000	Weak transcription	Psoas Muscle	Psoas
44	chr12:50644000-50651000	Weak transcription	Right Atrium	heart
45	chr12:50644000-50651200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:50644000-50652000	Weak transcription	Ovary	ovary
47	chr12:50644200-50648600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:50644200-50650000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:50644400-50646800	Weak transcription	HepG2	liver
50	chr12:50644400-50650000	Enhancers	Fetal Intestine Small	intestine

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