Variant report

Variant	rs7309519
Chromosome Location	chr12:50652280-50652281
allele	A/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	TCF12	chr12:50651373-50652284	A549	lung:	n/a	n/a
2	CREB1	chr12:50652046-50652380	A549	lung:	n/a	n/a
3	FOXA2	chr12:50651572-50652345	A549	lung:	n/a	n/a
4	NFIC	chr12:50651040-50652429	ECC-1	luminal epithelium:	n/a	n/a
5	CEBPB	chr12:50651683-50652304	Hela-S3	cervix:	n/a	chr12:50652137-50652148
6	NFIC	chr12:50650919-50652523	ECC-1	luminal epithelium:	n/a	n/a
7	NR3C1	chr12:50651690-50652398	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:50652124..50654779-chr12:50674069..50676173,2	K562	blood:
2	chr12:50650219..50652868-chr12:50794278..50797151,2	K562	blood:

Variant related genes	Relation type
RNU6-1093P	TF binding region
ENSG00000161813	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	0.88[AMR][1000 genomes]
rs10783342	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783343	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1362984	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862042	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2004283	0.87[AMR][1000 genomes]
rs2358538	0.83[EUR][1000 genomes]
rs4459386	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580732	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136648	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308692	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957659	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967954	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8181679	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9668955	0.92[AMR][1000 genomes];0.94[EUR][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
rs7309519	CERS5	cis	Nerve Tibial	GTEx
rs7309519	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50641000-50662000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:50641200-50653200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:50641400-50659600	Weak transcription	Esophagus	oesophagus
4	chr12:50648800-50668000	Weak transcription	Lung	lung
5	chr12:50649200-50665400	Weak transcription	Aorta	Aorta
6	chr12:50649200-50671000	Weak transcription	Small Intestine	intestine
7	chr12:50649600-50659600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:50650000-50654200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:50650400-50652400	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr12:50650400-50654600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr12:50650600-50653600	Enhancers	NHEK	skin
12	chr12:50650600-50654000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:50650800-50652400	Enhancers	HSMM	muscle
14	chr12:50650800-50654600	Enhancers	Stomach Mucosa	stomach
15	chr12:50650800-50655800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:50651000-50652400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:50651000-50652400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:50651000-50652400	Enhancers	Placenta	Placenta
19	chr12:50651000-50652400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr12:50651000-50652400	Enhancers	Psoas Muscle	Psoas
21	chr12:50651000-50652400	Enhancers	Right Atrium	heart
22	chr12:50651000-50652600	Enhancers	Fetal Muscle Leg	muscle
23	chr12:50651000-50652800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr12:50651000-50653000	Enhancers	HSMMtube	muscle
25	chr12:50651000-50653800	Enhancers	NHDF-Ad	bronchial
26	chr12:50651000-50654000	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr12:50651000-50654200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr12:50651000-50654600	Enhancers	HMEC	breast
29	chr12:50651000-50655600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:50651000-50655600	Enhancers	Duodenum Mucosa	Duodenum
31	chr12:50651200-50652400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:50651200-50652400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr12:50651200-50652400	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr12:50651200-50652400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:50651200-50652400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:50651200-50652400	Enhancers	Left Ventricle	heart
37	chr12:50651200-50652400	Enhancers	Rectal Smooth Muscle	rectum
38	chr12:50651200-50652400	Enhancers	HUVEC	blood vessel
39	chr12:50651200-50652600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:50651200-50652600	Enhancers	Pancreas	Pancrea
41	chr12:50651200-50653000	Enhancers	HepG2	liver
42	chr12:50651200-50653800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr12:50651200-50654000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:50651200-50654000	Enhancers	Osteobl	bone
45	chr12:50651400-50652400	Enhancers	Brain Hippocampus Middle	brain
46	chr12:50651400-50652400	Enhancers	Brain Substantia Nigra	brain
47	chr12:50651400-50652400	Enhancers	NHLF	lung
48	chr12:50651400-50654000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:50651400-50654000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:50651600-50652400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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