Variant report

Variant	rs12053980
Chromosome Location	chr3:195967495-195967496
allele	A/C
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	CEBPB	chr3:195967359-195967662	IMR90	lung:	n/a	chr3:195967512-195967523
2	CEBPB	chr3:195967365-195967616	HepG2	liver:	n/a	chr3:195967512-195967523
3	CEBPB	chr3:195967473-195967574	K562	blood:	n/a	chr3:195967512-195967523
4	CEBPB	chr3:195967357-195967609	HepG2	liver:	n/a	chr3:195967512-195967523
5	CEBPB	chr3:195967450-195967545	HepG2	liver:	n/a	chr3:195967512-195967523

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195965458..195967733-chr3:196012588..196015404,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO45-8	chr3:195967492-195967751	NONHSAT094310

Variant related genes	Relation type
PCYT1A	TF binding region
ENSG00000161217	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12490786	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632013	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35270876	0.86[ASN][1000 genomes]
rs56107869	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56152446	0.92[ASN][1000 genomes]
rs58820816	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771755	1.00[ASN][1000 genomes]
rs73084688	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73084691	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73084695	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086649	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648600	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9714228	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
7	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
10	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
11	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
12	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
13	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv878175	chr3:195907653-195973244	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv1014159	chr3:195908999-195968512	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
17	nsv878178	chr3:195929268-195998451	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv878179	chr3:195929268-196019680	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
19	nsv1014563	chr3:195934010-196085951	Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
20	nsv878180	chr3:195946535-196066569	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv878181	chr3:195946535-196072442	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
22	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
23	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:195948000-195970400	Strong transcription	Liver	Liver
3	chr3:195954800-195968600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:195955400-195968400	Weak transcription	Pancreas	Pancrea
5	chr3:195956000-195969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:195959400-195968600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:195959600-195978200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:195959800-195970000	Strong transcription	Duodenum Mucosa	Duodenum
9	chr3:195960000-195967600	Weak transcription	Hela-S3	cervix
10	chr3:195961000-195969800	Strong transcription	Fetal Muscle Leg	muscle
11	chr3:195961200-195969800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:195961200-195970400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:195961400-195969800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:195961600-195973800	Weak transcription	Stomach Mucosa	stomach
15	chr3:195962200-195969800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr3:195962200-195970000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:195962200-195970400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:195962400-195968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:195962400-195970600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:195962400-195977000	Strong transcription	Fetal Stomach	stomach
21	chr3:195962400-195979400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:195962600-195968200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:195962600-195968600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:195962600-195970400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:195962600-195970400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:195962800-195969800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:195962800-195970000	Strong transcription	Fetal Muscle Trunk	muscle
28	chr3:195962800-195970000	Strong transcription	NHEK	skin
29	chr3:195962800-195971200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:195963000-195969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:195963000-195970000	Strong transcription	Left Ventricle	heart
32	chr3:195963000-195970000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:195963200-195969800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:195963200-195970000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:195963200-195970400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:195963200-195970400	Strong transcription	Adipose Nuclei	Adipose
37	chr3:195963400-195968600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr3:195963400-195969800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:195963600-195969800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:195963600-195969800	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:195963600-195970400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:195963800-195967600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:195963800-195969400	Strong transcription	Primary B cells from cord blood	blood
44	chr3:195963800-195969400	Strong transcription	Brain Germinal Matrix	brain
45	chr3:195963800-195969800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:195963800-195969800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:195963800-195969800	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:195963800-195969800	Strong transcription	Placenta	Placenta
49	chr3:195963800-195969800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr3:195963800-195969800	Strong transcription	HMEC	breast

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