Variant report

Variant	rs1465788
Chromosome Location	chr14:69263599-69263600
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	EP300	chr14:69262333-69264410	K562	blood:	n/a	n/a
2	NFIC	chr14:69258747-69263739	GM12878	blood:	n/a	n/a
3	GATA1	chr14:69262430-69264491	PBDE	blood:	n/a	chr14:69263876-69263883 chr14:69263876-69263883 chr14:69263876-69263883 chr14:69263767-69263776 chr14:69263869-69263890
4	POLR2A	chr14:69257221-69263637	MCF10A-Er-Src	breast:	n/a	n/a
5	MTA3	chr14:69254975-69264454	GM12878	blood:	n/a	n/a
6	POLR2A	chr14:69256736-69263833	Raji	blood:	n/a	n/a
7	CHD2	chr14:69258414-69263620	Hela-S3	cervix:	n/a	chr14:69258897-69258907 chr14:69261411-69261421 chr14:69259834-69259844 chr14:69261032-69261042 chr14:69259118-69259128
8	FOS	chr14:69263400-69263677	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr14:69263460-69263715	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr14:69262397-69263657	Hela-S3	cervix:	n/a	chr14:69263347-69263358
11	IRF1	chr14:69262403-69263756	K562	blood:	n/a	n/a
12	MYC	chr14:69262281-69263620	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr14:69257288-69264495	PBDE	blood:	n/a	n/a
14	FOS	chr14:69263486-69263654	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr14:69263500-69263679	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr14:69255300-69263602	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAZ	chr14:69254887-69263779	IMR90	lung:	n/a	chr14:69258371-69258381 chr14:69257584-69257594
18	CEBPB	chr14:69260778-69263604	GM12878	blood:	n/a	chr14:69261397-69261409 chr14:69263347-69263358
19	CEBPB	chr14:69262658-69263677	H1-hESC	embryonic stem cell:	n/a	chr14:69263347-69263358
20	CTCF	chr14:69262061-69264029	A549	lung:	n/a	n/a
21	SP1	chr14:69259371-69263668	HCT-116	colon:	n/a	chr14:69259973-69259982 chr14:69259969-69259983 chr14:69259930-69259944 chr14:69259831-69259845 chr14:69261409-69261421 chr14:69259583-69259592 chr14:69261411-69261420 chr14:69259582-69259591 chr14:69260859-69260873 chr14:69259834-69259848 chr14:69259937-69259951 chr14:69259581-69259593 chr14:69261168-69261180 chr14:69259581-69259593 chr14:69259926-69259935 chr14:69261409-69261421 chr14:69259972-69259984
22	POLR2A	chr14:69251917-69264005	GM12878	blood:	n/a	n/a
23	MYC	chr14:69263510-69263620	MCF10A-Er-Src	breast:	n/a	n/a
24	CREB1	chr14:69255257-69263615	GM12878	blood:	n/a	chr14:69260175-69260188
25	JUND	chr14:69262200-69263650	H1-hESC	embryonic stem cell:	n/a	n/a
26	SP1	chr14:69262700-69264485	H1-hESC	embryonic stem cell:	n/a	chr14:69263668-69263682
27	ZMIZ1	chr14:69263445-69264435	K562	blood:	n/a	n/a
28	RUNX3	chr14:69258444-69263720	GM12878	blood:	n/a	n/a
29	JUN	chr14:69262181-69264453	K562	blood:	n/a	n/a
30	CEBPB	chr14:69263265-69263610	IMR90	lung:	n/a	chr14:69263347-69263358
31	POLR2A	chr14:69254876-69264506	H1-hESC	embryonic stem cell:	n/a	n/a
32	SIN3A	chr14:69257301-69264370	H1-hESC	embryonic stem cell:	n/a	chr14:69260510-69260521
33	POLR2A	chr14:69252398-69264017	GM12878	blood:	n/a	n/a
34	NR2F2	chr14:69263531-69264434	K562	blood:	n/a	n/a
35	BACH1	chr14:69263558-69264069	K562	blood:	n/a	n/a
36	POLR2A	chr14:69252090-69264348	GM12891	blood:	n/a	n/a
37	MTA3	chr14:69262164-69263832	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr14:69262381-69264542	K562	blood:	n/a	n/a
39	CUX1	chr14:69263070-69264003	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:69090615..69103406-chr14:69249821..69264188,29	MCF-7	breast:
2	chr14:68140439..68142137-chr14:69262660..69264249,2	MCF-7	breast:
3	chr14:69262582..69264227-chr20:45984862..45986463,2	MCF-7	breast:
4	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
5	chr14:69091753..69104091-chr14:69256141..69263760,20	MCF-7	breast:
6	chr14:69258720..69263996-chr17:57918463..57922385,5	MCF-7	breast:

Variant related genes	Relation type
ZFP36L1	TF binding region
ENSG00000199004	Chromatin interaction
ENSG00000182185	Chromatin interaction
ENSG00000100568	Chromatin interaction
ENSG00000259038	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10142466	0.95[ASN][1000 genomes]
rs11626883	0.95[ASN][1000 genomes]
rs12889006	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1595260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1595261	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17106304	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17835641	0.95[ASN][1000 genomes]
rs17835647	0.95[ASN][1000 genomes]
rs1836984	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs194748	0.92[ASN][1000 genomes]
rs194749	0.97[ASN][1000 genomes]
rs194751	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194778	0.81[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2236262	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2236263	0.86[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34489253	0.98[ASN][1000 genomes]
rs367677	0.89[ASN][1000 genomes]
rs3742887	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825568	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4899258	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899259	0.92[ASN][1000 genomes]
rs4902647	0.80[JPT][hapmap]
rs4902651	0.95[ASN][1000 genomes]
rs6573857	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7146217	0.84[JPT][hapmap];0.82[LWK][hapmap];0.81[YRI][hapmap]
rs7149271	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156516	0.92[ASN][1000 genomes]
rs8011558	0.81[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs8022092	0.98[ASN][1000 genomes]
rs927292	0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035267	chr14:69230254-69348126	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv542123	chr14:69230254-69348126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv902070	chr14:69244214-69308182	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Type 1 diabetes	19430480	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465788	ZFP36L1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69257200-69263600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
2	chr14:69257200-69263800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr14:69262600-69263600	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr14:69262600-69263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr14:69262600-69264200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:69262800-69263600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr14:69262800-69263600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:69262800-69263600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:69262800-69263600	Active TSS	Brain Hippocampus Middle	brain
10	chr14:69262800-69263600	Flanking Active TSS	Brain Substantia Nigra	brain
11	chr14:69262800-69263800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr14:69263000-69263600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr14:69263000-69263600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr14:69263000-69263600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr14:69263000-69263600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr14:69263000-69263600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:69263000-69263600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr14:69263000-69263600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr14:69263000-69263600	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr14:69263000-69263600	Flanking Active TSS	Fetal Lung	lung
21	chr14:69263000-69263600	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr14:69263000-69263600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr14:69263000-69263600	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr14:69263000-69263600	Flanking Active TSS	Thymus	Thymus
25	chr14:69263000-69263600	Flanking Active TSS	GM12878-XiMat	blood
26	chr14:69263000-69263800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr14:69263000-69263800	Flanking Active TSS	Hela-S3	cervix
28	chr14:69263000-69263800	Flanking Active TSS	NHEK	skin
29	chr14:69263000-69264000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:69263000-69264200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr14:69263000-69264400	Flanking Active TSS	K562	blood
32	chr14:69263200-69263600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr14:69263200-69263600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr14:69263200-69263600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr14:69263200-69263600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr14:69263200-69263600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr14:69263200-69263600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:69263200-69263600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr14:69263200-69263600	Enhancers	Brain Cingulate Gyrus	brain
40	chr14:69263200-69263600	Active TSS	Fetal Brain Male	brain
41	chr14:69263200-69263600	Enhancers	Fetal Kidney	kidney
42	chr14:69263200-69263600	Active TSS	Skeletal Muscle Female	skeletal muscle
43	chr14:69263200-69263600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr14:69263200-69263800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr14:69263200-69263800	Enhancers	Pancreas	Pancrea
46	chr14:69263200-69263800	Enhancers	Spleen	Spleen
47	chr14:69263200-69263800	Flanking Active TSS	HepG2	liver
48	chr14:69263200-69263800	Enhancers	HSMMtube	muscle
49	chr14:69263200-69264000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr14:69263200-69264000	Weak transcription	Esophagus	oesophagus

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