Variant report

Variant	rs12824259
Chromosome Location	chr12:65087384-65087385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65082782..65085440-chr12:65086852..65090149,3	MCF-7	breast:
2	chr12:65018895..65020884-chr12:65086015..65088325,2	MCF-7	breast:
3	chr12:65002182..65006670-chr12:65087134..65093452,10	MCF-7	breast:
4	chr12:65002687..65005159-chr12:65085153..65088192,5	MCF-7	breast:
5	chr12:65071734..65074838-chr12:65083895..65087734,4	MCF-7	breast:
6	chr12:65002975..65007733-chr12:65085361..65090240,7	K562	blood:
7	chr12:65081919..65084016-chr12:65085608..65087815,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153179	Chromatin interaction
ENSG00000256670	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17100618	1.00[CEU][hapmap]
rs35005876	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61932664	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73323424	0.85[AFR][1000 genomes]
rs8648	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv899210	chr12:65076498-65184236	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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 target site	13 gene(s)	inside rSNPs	diseases
9	nsv524627	chr12:65082330-65091031	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65070000-65092400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:65075000-65108400	Weak transcription	NH-A	brain
3	chr12:65075200-65087400	Weak transcription	HMEC	breast
4	chr12:65075400-65088600	Weak transcription	Esophagus	oesophagus
5	chr12:65077000-65091800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:65077200-65088200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:65077200-65088600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:65077200-65091800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:65077200-65106800	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:65077400-65088600	Weak transcription	Ovary	ovary
11	chr12:65077400-65091800	Weak transcription	Brain Anterior Caudate	brain
12	chr12:65077400-65114800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:65077600-65091800	Weak transcription	Brain Substantia Nigra	brain
14	chr12:65078600-65088600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr12:65078600-65089200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:65078600-65092200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:65078800-65092400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:65079000-65092000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:65079200-65091600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:65079200-65092200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr12:65079800-65087800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:65080000-65113600	Weak transcription	Colonic Mucosa	Colon
23	chr12:65081800-65100400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr12:65082000-65088200	Weak transcription	Stomach Mucosa	stomach
25	chr12:65082000-65089600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:65082400-65088200	Weak transcription	NHEK	skin
27	chr12:65082400-65088400	Weak transcription	Small Intestine	intestine
28	chr12:65082400-65090400	Genic enhancers	Primary T cells fromperipheralblood	blood
29	chr12:65082400-65094400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:65082600-65088000	Weak transcription	Thymus	Thymus
31	chr12:65082600-65088200	Weak transcription	Aorta	Aorta
32	chr12:65082800-65087400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:65082800-65087400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:65082800-65087400	Weak transcription	Left Ventricle	heart
35	chr12:65082800-65087600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:65082800-65087600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:65082800-65088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:65082800-65088000	Weak transcription	Right Ventricle	heart
39	chr12:65082800-65088200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:65082800-65088200	Weak transcription	Gastric	stomach
41	chr12:65082800-65088200	Weak transcription	Pancreas	Pancrea
42	chr12:65082800-65088600	Weak transcription	NHLF	lung
43	chr12:65083200-65089600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr12:65084200-65091200	Genic enhancers	Primary T cells from cord blood	blood
45	chr12:65084400-65087800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:65084600-65090600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:65085000-65088000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr12:65085000-65089600	Strong transcription	Primary B cells from cord blood	blood
49	chr12:65085000-65089800	Strong transcription	Placenta	Placenta
50	chr12:65085000-65090200	Strong transcription	Dnd41	blood

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