Variant report

Variant	rs12299208
Chromosome Location	chr12:117375274-117375275
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	chr12:117373255..117375339-chr12:117377275..117379604,2	MCF-7	breast:

Extended variants
information (count: 32 )
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];0.96[AFR][1000 genomes]
rs11068257	1.00[AMR][1000 genomes]
rs11068261	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11068284	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs11068291	1.00[AMR][1000 genomes]
rs12296579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297294	1.00[AMR][1000 genomes]
rs12299197	1.00[AMR][1000 genomes]
rs12303371	1.00[YRI][hapmap];0.91[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12308160	1.00[AMR][1000 genomes]
rs12308162	1.00[AMR][1000 genomes]
rs12309933	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12309993	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12310473	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311443	1.00[YRI][hapmap];0.91[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];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61193113	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7300401	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7309036	0.87[AFR][1000 genomes]
rs7309550	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	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	nsv1046811	chr12:117353904-117396230	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
3	esv1798657	chr12:117354067-117392259	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
4	nsv1048942	chr12:117365506-117400588	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117354800-117383200	Weak transcription	Esophagus	oesophagus
2	chr12:117358400-117392600	Weak transcription	Small Intestine	intestine
3	chr12:117363200-117399400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:117363400-117381000	Weak transcription	NHEK	skin
5	chr12:117363400-117381400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:117363400-117385000	Weak transcription	HUVEC	blood vessel
7	chr12:117365000-117383200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:117365000-117383400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:117365000-117406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:117365800-117381200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:117365800-117383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:117366000-117375600	Strong transcription	Primary T cells from cord blood	blood
13	chr12:117366200-117377600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:117366600-117381000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:117366600-117381200	Weak transcription	Liver	Liver
16	chr12:117366600-117381400	Weak transcription	Aorta	Aorta
17	chr12:117366600-117383200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:117366600-117388400	Weak transcription	K562	blood
19	chr12:117367000-117380000	Weak transcription	Fetal Thymus	thymus
20	chr12:117367200-117379200	Weak transcription	Spleen	Spleen
21	chr12:117367800-117382800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:117368000-117379800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:117368000-117381200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:117368000-117383200	Weak transcription	Hela-S3	cervix
25	chr12:117368000-117383400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:117368200-117376400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr12:117368200-117383000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:117368800-117381400	Weak transcription	Adipose Nuclei	Adipose
29	chr12:117369200-117376400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:117369800-117383200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr12:117370000-117382000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:117371400-117381000	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:117371400-117381200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:117371400-117381200	Weak transcription	Brain Substantia Nigra	brain
35	chr12:117371400-117381600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:117371400-117383400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:117371400-117383400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:117371600-117378200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr12:117371600-117380000	Weak transcription	Brain Angular Gyrus	brain
40	chr12:117371800-117381000	Weak transcription	Brain Germinal Matrix	brain
41	chr12:117372000-117375600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr12:117372000-117377200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:117372200-117377200	Weak transcription	HSMMtube	muscle
44	chr12:117372200-117377600	Weak transcription	Psoas Muscle	Psoas
45	chr12:117372200-117380600	Weak transcription	Fetal Brain Female	brain
46	chr12:117372400-117381400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:117372400-117383000	Weak transcription	NH-A	brain
48	chr12:117372600-117375400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:117372600-117375400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:117372600-117375400	Strong transcription	Dnd41	blood

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