Variant report

Variant	rs12296749
Chromosome Location	chr12:65013565-65013566
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	CEBPB	chr12:65013539-65014121	K562	blood:	n/a	n/a
2	PML	chr12:65012736-65013610	GM12878	blood:	n/a	n/a
3	CEBPB	chr12:65012610-65014099	K562	blood:	n/a	chr12:65013308-65013325
4	CHD1	chr12:65012870-65013579	GM12878	blood:	n/a	n/a
5	CBX3	chr12:65012836-65013581	K562	blood:	n/a	n/a
6	WRNIP1	chr12:65012849-65013663	GM12878	blood:	n/a	n/a
7	CEBPB	chr12:65012889-65013765	Hela-S3	cervix:	n/a	chr12:65013308-65013325

No.	Distal block	Cell Line	Cell type
1	chr12:65013129..65015693-chr12:65017473..65019068,2	K562	blood:
2	chr12:65013056..65015741-chr12:65019440..65021647,2	MCF-7	breast:
3	chr12:65011462..65014885-chr12:65017332..65020916,6	MCF-7	breast:
4	chr12:65001678..65008078-chr12:65013108..65023657,17	MCF-7	breast:
5	chr12:65011593..65014021-chr12:65067404..65069519,2	K562	blood:

Variant related genes	Relation type
MIR548C	TF binding region
ENSG00000153179	Chromatin interaction
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10128936	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12311754	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17176378	0.82[ASN][1000 genomes]
rs35648703	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35947911	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4495970	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56061516	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61463437	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832443	chr12:64878856-65057265	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1048199	chr12:64951666-65021700	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
3	nsv541512	chr12:64951666-65021700	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
4	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking 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 miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65005800-65015200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:65005800-65017800	Weak transcription	Gastric	stomach
3	chr12:65006200-65017400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:65006200-65017600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:65006200-65018800	Weak transcription	Fetal Thymus	thymus
6	chr12:65006200-65019000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:65006200-65019000	Weak transcription	NHEK	skin
8	chr12:65006200-65019400	Weak transcription	Psoas Muscle	Psoas
9	chr12:65006400-65017000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:65006600-65017400	Weak transcription	Small Intestine	intestine
11	chr12:65006600-65018200	Weak transcription	Fetal Intestine Large	intestine
12	chr12:65006800-65031800	Weak transcription	Dnd41	blood
13	chr12:65007000-65014800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:65007000-65018800	Weak transcription	HMEC	breast
15	chr12:65007000-65019200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:65007200-65015000	Weak transcription	HepG2	liver
17	chr12:65007200-65017600	Weak transcription	Stomach Mucosa	stomach
18	chr12:65007800-65017600	Weak transcription	Lung	lung
19	chr12:65008600-65019000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:65009200-65019200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:65009800-65019200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:65009800-65019400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:65010000-65023200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:65010200-65019400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:65010400-65017000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:65010400-65017000	Weak transcription	NH-A	brain
27	chr12:65010400-65018200	Weak transcription	Colonic Mucosa	Colon
28	chr12:65010400-65019000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:65010600-65017800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:65010600-65018800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:65010600-65018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr12:65010600-65018800	Weak transcription	Fetal Lung	lung
33	chr12:65010600-65019000	Weak transcription	Fetal Stomach	stomach
34	chr12:65010800-65013800	Enhancers	HUVEC	blood vessel
35	chr12:65010800-65018600	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:65010800-65022200	Weak transcription	Spleen	Spleen
37	chr12:65011000-65018400	Weak transcription	Brain Substantia Nigra	brain
38	chr12:65011200-65018800	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:65011600-65014200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:65011600-65019000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:65011800-65019000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:65012000-65016600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr12:65012000-65017600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:65012200-65013600	Enhancers	Pancreas	Pancrea
45	chr12:65012400-65018200	Weak transcription	Fetal Intestine Small	intestine
46	chr12:65012400-65019200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:65012600-65013600	Enhancers	Brain Hippocampus Middle	brain
48	chr12:65012600-65013800	Enhancers	Placenta	Placenta
49	chr12:65012600-65019200	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:65012800-65013600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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