Variant report

Variant	rs3212260
Chromosome Location	chr14:24804088-24804089
allele	A/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	ZNF143	chr14:24804040-24804377	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr14:24803858-24804539	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr14:24802594-24804686	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr14:24803569-24804526	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr14:24802603-24804394	SK-N-SH	brain:	n/a	chr14:24803292-24803305 chr14:24802991-24803007 chr14:24802993-24803006 chr14:24802995-24803005 chr14:24804354-24804367 chr14:24803037-24803046 chr14:24802990-24803008
6	POLR2A	chr14:24802615-24805178	HUVEC	blood vessel:	n/a	n/a
7	SIN3A	chr14:24804004-24804302	H1-hESC	embryonic stem cell:	n/a	n/a
8	BACH1	chr14:24803932-24804345	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr14:24803946-24804506	HUVEC	blood vessel:	n/a	n/a
10	YY1	chr14:24804027-24804366	H1-hESC	embryonic stem cell:	n/a	chr14:24804315-24804326 chr14:24804315-24804324 chr14:24804310-24804324 chr14:24804203-24804214 chr14:24804191-24804205

No.	Distal block	Cell Line	Cell type
1	chr14:24802266..24804821-chr14:24805922..24808045,3	K562	blood:
2	chr14:24796879..24804920-chr14:24831628..24840088,12	MCF-7	breast:
3	chr14:24796718..24800207-chr14:24803965..24807105,3	MCF-7	breast:
4	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
5	chr14:24709884..24713728-chr14:24799730..24804763,6	MCF-7	breast:
6	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
7	chr14:24803661..24805578-chr14:24807953..24810050,2	K562	blood:
8	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
9	chr14:24801703..24804412-chr14:24880486..24883068,2	MCF-7	breast:
10	chr14:24800598..24804207-chr14:24909756..24912911,5	K562	blood:

Variant related genes	Relation type
ADCY4	TF binding region
ENSG00000100968	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000129467	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10459527	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1109152	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1109153	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12050389	0.86[ASN][1000 genomes]
rs12433338	0.86[ASN][1000 genomes]
rs12436194	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12436417	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12881276	0.81[ASN][1000 genomes]
rs17184689	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2295300	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2332325	0.87[ASN][1000 genomes]
rs2877642	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3181251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212242	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212243	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8008406	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8014112	0.81[ASN][1000 genomes]
rs882726	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv564060	chr14:24776401-24809795	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3212260	LTB4R	cis	Thyroid	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24801200-24804800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr14:24801400-24804600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr14:24801800-24804400	Bivalent Enhancer	Fetal Lung	lung
4	chr14:24801800-24804600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr14:24801800-24805400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr14:24802000-24804200	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr14:24802000-24804400	Active TSS	Osteobl	bone
8	chr14:24802200-24804600	Active TSS	Right Atrium	heart
9	chr14:24802400-24804400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:24802600-24804200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
11	chr14:24802600-24804400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr14:24802600-24804600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr14:24802800-24804200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
14	chr14:24802800-24804200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
15	chr14:24802800-24804200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
16	chr14:24802800-24804200	Active TSS	NHDF-Ad	bronchial
17	chr14:24802800-24804400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:24802800-24804400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:24802800-24804400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr14:24802800-24804600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
21	chr14:24802800-24804800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr14:24802800-24804800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr14:24802800-24805000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
24	chr14:24802800-24805200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
25	chr14:24803000-24804200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
26	chr14:24803000-24804200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
27	chr14:24803000-24804400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
28	chr14:24803000-24804400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr14:24803000-24804400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
30	chr14:24803000-24804400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
31	chr14:24803000-24804400	Bivalent/Poised TSS	HSMM	muscle
32	chr14:24803000-24804600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr14:24803000-24804600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:24803000-24804600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
35	chr14:24803000-24804600	Active TSS	Ovary	ovary
36	chr14:24803000-24804800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
37	chr14:24803000-24804800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr14:24803000-24804800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
39	chr14:24803000-24804800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
40	chr14:24803000-24805400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr14:24803200-24804200	Bivalent Enhancer	Fetal Brain Male	brain
42	chr14:24803200-24804400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:24803200-24804400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr14:24803200-24804400	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr14:24803200-24804600	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
46	chr14:24803400-24804200	Flanking Active TSS	Esophagus	oesophagus
47	chr14:24803400-24804400	Flanking Active TSS	Spleen	Spleen
48	chr14:24803400-24804400	Bivalent/Poised TSS	NH-A	brain
49	chr14:24803400-24804600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr14:24803400-24804600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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