Variant report

Variant	rs12309933
Chromosome Location	chr12:117423422-117423423
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117421809..117423733-chr12:117438090..117440215,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11068227	1.00[AMR][1000 genomes]
rs11068229	1.00[AMR][1000 genomes]
rs11068244	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11068257	1.00[AMR][1000 genomes]
rs11068261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11068284	0.88[YRI][hapmap];0.92[AFR][1000 genomes]
rs11068291	1.00[AMR][1000 genomes]
rs12296579	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297294	1.00[AMR][1000 genomes]
rs12299197	1.00[AMR][1000 genomes]
rs12299208	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300945	1.00[YRI][hapmap]
rs12303371	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12304848	1.00[AMR][1000 genomes]
rs12306116	1.00[AMR][1000 genomes]
rs12307625	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12308160	1.00[AMR][1000 genomes]
rs12308162	1.00[AMR][1000 genomes]
rs12309993	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310473	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311443	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313091	1.00[AMR][1000 genomes]
rs12316781	1.00[AMR][1000 genomes]
rs12319981	1.00[AMR][1000 genomes]
rs12322115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61193113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7300401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7309550	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][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	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117384600-117427400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:117384800-117450400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:117387800-117463600	Weak transcription	HMEC	breast
4	chr12:117393800-117471000	Weak transcription	Small Intestine	intestine
5	chr12:117397000-117429200	Weak transcription	Right Ventricle	heart
6	chr12:117397000-117442400	Weak transcription	Colonic Mucosa	Colon
7	chr12:117404600-117427000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:117404600-117442400	Weak transcription	HepG2	liver
9	chr12:117404800-117426400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:117405600-117442400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:117408000-117427600	Weak transcription	Dnd41	blood
12	chr12:117408200-117424800	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:117408200-117426400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr12:117408200-117427000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:117408200-117429600	Weak transcription	Brain Substantia Nigra	brain
16	chr12:117408200-117442400	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:117408400-117432600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:117408400-117452200	Weak transcription	Thymus	Thymus
19	chr12:117409000-117427200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:117411000-117424400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:117411600-117425600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:117411600-117426800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:117411600-117427200	Weak transcription	Fetal Kidney	kidney
24	chr12:117411600-117427600	Weak transcription	A549	lung
25	chr12:117411600-117434000	Weak transcription	Brain Angular Gyrus	brain
26	chr12:117411600-117451800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:117411800-117429200	Weak transcription	Hela-S3	cervix
28	chr12:117412000-117424800	Weak transcription	Liver	Liver
29	chr12:117412000-117424800	Weak transcription	Left Ventricle	heart
30	chr12:117412000-117426000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:117412000-117426200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:117412000-117426800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:117412000-117427000	Weak transcription	Pancreas	Pancrea
34	chr12:117412000-117427600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr12:117412000-117427600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:117412000-117432400	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:117412200-117425200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:117412200-117432600	Weak transcription	Spleen	Spleen
39	chr12:117412200-117440000	Weak transcription	Esophagus	oesophagus
40	chr12:117413400-117424800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:117416200-117426200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:117416200-117427000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:117416600-117426000	Weak transcription	Primary B cells from cord blood	blood
44	chr12:117417200-117452400	Weak transcription	Psoas Muscle	Psoas
45	chr12:117417400-117426800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:117417400-117453600	Weak transcription	GM12878-XiMat	blood
47	chr12:117418000-117427000	Weak transcription	Fetal Thymus	thymus
48	chr12:117418000-117427800	Weak transcription	HSMM	muscle
49	chr12:117418000-117433800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr12:117418000-117433800	Weak transcription	Lung	lung

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