Variant report

Variant	rs12296993
Chromosome Location	chr12:117217720-117217721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117208783..117211588-chr12:117216119..117217810,2	MCF-7	breast:
2	chr12:117217330..117219094-chr12:117250590..117252479,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10850709	0.82[ASN][1000 genomes]
rs10850710	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10850711	0.84[ASN][1000 genomes]
rs10850713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10850716	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068174	0.90[ASN][1000 genomes]
rs11068177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068182	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068184	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11068185	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068187	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068188	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068189	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068190	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068191	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068192	0.94[ASN][1000 genomes]
rs11503182	0.82[ASN][1000 genomes]
rs12231554	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231952	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12302528	0.82[ASN][1000 genomes]
rs12305605	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12308877	0.82[ASN][1000 genomes]
rs12309159	0.98[ASN][1000 genomes]
rs12312295	0.98[ASN][1000 genomes]
rs12314176	0.82[ASN][1000 genomes]
rs12322695	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12426049	0.98[ASN][1000 genomes]
rs34454980	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56174906	0.82[ASN][1000 genomes]
rs56692573	0.98[ASN][1000 genomes]
rs58367668	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137138	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307465	1.00[ASN][1000 genomes]
rs73405110	1.00[EUR][1000 genomes];0.94[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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers 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 target site	19 gene(s)	inside rSNPs	diseases
2	nsv1048004	chr12:117170738-117219076	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	nsv1039046	chr12:117170989-117225635	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117177000-117224400	Weak transcription	Brain Substantia Nigra	brain
2	chr12:117177200-117221000	Weak transcription	Fetal Brain Male	brain
3	chr12:117177400-117225800	Weak transcription	HepG2	liver
4	chr12:117191200-117221000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:117198000-117256200	Weak transcription	Hela-S3	cervix
6	chr12:117198200-117233600	Weak transcription	Fetal Stomach	stomach
7	chr12:117198200-117236600	Weak transcription	A549	lung
8	chr12:117198600-117223800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:117198600-117233600	Weak transcription	Right Atrium	heart
10	chr12:117198800-117220800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:117209800-117232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:117211800-117218000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:117213400-117226600	Weak transcription	Fetal Intestine Small	intestine
14	chr12:117213800-117223400	Weak transcription	Placenta	Placenta
15	chr12:117215800-117221400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:117216000-117222000	Weak transcription	K562	blood
17	chr12:117216200-117222800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr12:117216200-117225400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:117216400-117218800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:117216600-117218600	Strong transcription	Fetal Thymus	thymus
21	chr12:117216600-117219600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:117216600-117220600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:117216600-117226800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:117216800-117219200	Strong transcription	Brain Hippocampus Middle	brain
25	chr12:117216800-117219400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:117216800-117219800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:117216800-117219800	Strong transcription	Dnd41	blood
28	chr12:117216800-117223200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:117216800-117223600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:117216800-117223600	Strong transcription	Fetal Brain Female	brain
31	chr12:117216800-117224400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:117216800-117225400	Strong transcription	Brain Germinal Matrix	brain
33	chr12:117216800-117225600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr12:117216800-117225600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:117216800-117229600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:117217000-117218200	Strong transcription	GM12878-XiMat	blood
37	chr12:117217000-117218600	Strong transcription	Primary B cells from cord blood	blood
38	chr12:117217000-117219000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr12:117217000-117219000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr12:117217000-117219200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:117217000-117219200	Strong transcription	Brain Angular Gyrus	brain
42	chr12:117217000-117219400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:117217000-117219600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:117217000-117219600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:117217000-117219600	Strong transcription	Brain Anterior Caudate	brain
46	chr12:117217000-117219800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr12:117217000-117222200	Strong transcription	Thymus	Thymus
48	chr12:117217000-117222400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr12:117217000-117223400	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr12:117217200-117219600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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