Variant report

Variant	rs14259
Chromosome Location	chr12:122353796-122353797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122331116..122333896-chr12:122352806..122354784,2	MCF-7	breast:
2	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
3	chr12:122353628..122357829-chr12:122368964..122373628,4	MCF-7	breast:
4	chr12:122352837..122354864-chr12:122355521..122357983,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110987	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000110801	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1168658	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1168661	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1169081	0.80[EUR][1000 genomes]
rs1177588	0.83[ASN][1000 genomes]
rs12578258	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579389	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579730	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375653	0.83[ASN][1000 genomes]
rs1375654	0.83[ASN][1000 genomes]
rs1375655	0.83[ASN][1000 genomes]
rs1630699	0.83[ASN][1000 genomes]
rs1667586	0.83[ASN][1000 genomes]
rs1678952	0.83[ASN][1000 genomes]
rs1678953	0.83[ASN][1000 genomes]
rs1720030	0.83[ASN][1000 genomes]
rs1720066	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1720068	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17852561	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2272135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309275	0.81[EUR][1000 genomes]
rs2442439	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688409	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34506529	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34930953	0.87[AMR][1000 genomes]
rs35252940	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825172	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4069666	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4760108	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs482421	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs483416	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs508395	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55826938	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56177852	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58379261	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59517025	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59972569	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs686220	0.83[ASN][1000 genomes]
rs7309105	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7313748	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs876934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122328200-122355600	Weak transcription	Fetal Brain Male	brain
2	chr12:122328400-122355600	Strong transcription	Fetal Stomach	stomach
3	chr12:122329600-122355800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:122329600-122355800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:122329800-122355000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:122330400-122355800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr12:122330600-122353800	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:122331000-122355000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:122331600-122355600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:122332000-122354600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:122332000-122356600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:122332400-122355600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:122332400-122355600	Strong transcription	Fetal Intestine Small	intestine
14	chr12:122332400-122355800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:122332600-122355400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:122332600-122355600	Strong transcription	Fetal Intestine Large	intestine
17	chr12:122332800-122355000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:122332800-122355400	Strong transcription	Liver	Liver
19	chr12:122332800-122355600	Strong transcription	Duodenum Mucosa	Duodenum
20	chr12:122333000-122356000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:122336400-122356000	Strong transcription	Adipose Nuclei	Adipose
22	chr12:122338000-122356000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:122341000-122356000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr12:122341400-122355800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr12:122341600-122356000	Weak transcription	Fetal Heart	heart
26	chr12:122341600-122356600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:122341800-122355600	Weak transcription	Stomach Mucosa	stomach
28	chr12:122342200-122356000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:122343200-122353800	Weak transcription	Small Intestine	intestine
30	chr12:122344000-122355800	Strong transcription	Brain Germinal Matrix	brain
31	chr12:122344200-122355800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:122344400-122356400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:122345400-122353800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:122345400-122356000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:122345600-122355600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:122345600-122355800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:122345800-122353800	Strong transcription	Fetal Lung	lung
38	chr12:122346200-122355800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:122346600-122356000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:122347000-122355600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:122347000-122355800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:122347200-122355600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr12:122347200-122356000	Weak transcription	Psoas Muscle	Psoas
44	chr12:122347800-122354000	Weak transcription	Right Ventricle	heart
45	chr12:122347800-122356000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr12:122347800-122356000	Weak transcription	Brain Angular Gyrus	brain
47	chr12:122348000-122353800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:122348000-122354200	Weak transcription	Esophagus	oesophagus
49	chr12:122348000-122355800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:122348800-122355200	Strong transcription	Brain Cingulate Gyrus	brain

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