Variant report

Variant	rs6580728
Chromosome Location	chr12:50541127-50541128
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	MAFK	chr12:50541081-50541451	Hela-S3	cervix:	n/a	chr12:50541259-50541274
2	MAFF	chr12:50541080-50541455	K562	blood:	n/a	chr12:50541258-50541276
3	MAFK	chr12:50541027-50541574	GM12878	blood:	n/a	chr12:50541259-50541274
4	MAFK	chr12:50541075-50541471	IMR90	lung:	n/a	chr12:50541259-50541274
5	MAFK	chr12:50541075-50541451	HepG2	liver:	n/a	chr12:50541259-50541274
6	MAFK	chr12:50541082-50541478	H1-hESC	embryonic stem cell:	n/a	chr12:50541259-50541274
7	MAFF	chr12:50541077-50541464	HepG2	liver:	n/a	chr12:50541258-50541276
8	MAFK	chr12:50541082-50541452	HepG2	liver:	n/a	chr12:50541259-50541274
9	MAFK	chr12:50541081-50541448	K562	blood:	n/a	chr12:50541259-50541274

No.	Distal block	Cell Line	Cell type
1	chr12:50535564..50538252-chr12:50540355..50542372,2	MCF-7	breast:
2	chr12:50539829..50542796-chr12:50543906..50546039,2	MCF-7	breast:
3	chr12:50535984..50537611-chr12:50539393..50542341,2	K562	blood:
4	chr12:50533908..50538982-chr12:50540914..50544444,4	MCF-7	breast:

Variant related genes	Relation type
CERS5	TF binding region
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10735824	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783338	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876000	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169278	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169281	0.96[CEU][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169282	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12369049	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12369104	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12819883	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554844	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554845	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124432	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2204683	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3184122	0.83[CEU][hapmap]
rs34167640	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3741562	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59262224	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66782120	0.88[ASN][1000 genomes]
rs7135322	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138945	0.96[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7294618	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307230	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307469	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7308474	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7398567	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7961065	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7961112	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7964698	0.86[EUR][1000 genomes]
rs7967979	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7968119	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7972465	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7978904	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9364	0.88[CEU][hapmap]

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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	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
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6580728	CERS5	cis	Nerve Tibial	GTEx
rs6580728	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs6580728	CERS5	cis	Muscle Skeletal	GTEx
rs6580728	KIAA1463	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
3	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
4	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:50529800-50543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:50529800-50559800	Weak transcription	NHLF	lung
8	chr12:50530000-50559600	Weak transcription	A549	lung
9	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
10	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
11	chr12:50531600-50543200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
14	chr12:50531800-50554400	Weak transcription	K562	blood
15	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
16	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
17	chr12:50532000-50560200	Weak transcription	Gastric	stomach
18	chr12:50532400-50541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:50532400-50541400	Weak transcription	Liver	Liver
20	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
21	chr12:50532800-50542200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:50533200-50544800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:50534600-50544800	Weak transcription	Ovary	ovary
27	chr12:50535000-50545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:50535200-50541800	Weak transcription	Lung	lung
29	chr12:50535200-50545000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
32	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:50536800-50545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:50537000-50544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
38	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:50537400-50543000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr12:50537800-50544600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:50537800-50545000	Weak transcription	HMEC	breast
47	chr12:50537800-50545200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:50537800-50545200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:50537800-50547400	Weak transcription	Primary T cells from cord blood	blood
50	chr12:50537800-50550400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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