Variant report

Variant	rs1972801
Chromosome Location	chr12:83377227-83377228
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	chr12:83376935..83379411-chr12:83411296..83413142,2	MCF-7	breast:
2	chr12:83369189..83370820-chr12:83374868..83377615,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10746262	0.94[EUR][1000 genomes]
rs10778918	0.92[EUR][1000 genomes]
rs10778921	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1434425	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1655611	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1655612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1682567	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1682575	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1682579	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1682580	0.98[EUR][1000 genomes]
rs1682606	0.94[EUR][1000 genomes]
rs1682607	0.82[EUR][1000 genomes]
rs1682608	0.94[EUR][1000 genomes]
rs1796150	0.90[EUR][1000 genomes]
rs1796157	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796161	0.94[EUR][1000 genomes]
rs1796162	0.94[EUR][1000 genomes]
rs1796166	0.90[EUR][1000 genomes]
rs1796167	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1796168	0.94[EUR][1000 genomes]
rs1796178	0.90[EUR][1000 genomes]
rs1796187	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1796296	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796300	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1821444	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2046417	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2062357	0.94[EUR][1000 genomes]
rs2403025	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2403026	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2707753	0.94[EUR][1000 genomes]
rs2707754	0.94[EUR][1000 genomes]
rs2707760	0.88[EUR][1000 genomes]
rs2708000	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4882531	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6539697	0.94[EUR][1000 genomes]
rs7297707	0.88[EUR][1000 genomes]
rs7299175	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303058	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953974	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv1047239	chr12:83362299-83444855	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83347000-83379600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:83356200-83379400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:83356400-83381600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:83356600-83381400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:83357800-83389600	Weak transcription	Fetal Intestine Large	intestine
6	chr12:83358000-83389600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain
9	chr12:83358600-83379400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:83358600-83394200	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:83358600-83399600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:83358600-83409400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:83362000-83382200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:83364200-83379600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:83367000-83379400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:83367400-83391800	Weak transcription	Small Intestine	intestine
17	chr12:83367600-83379400	Weak transcription	Brain Substantia Nigra	brain
18	chr12:83368800-83379600	Weak transcription	Fetal Lung	lung
19	chr12:83368800-83386800	Weak transcription	Fetal Stomach	stomach
20	chr12:83368800-83393800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:83368800-83399200	Weak transcription	Esophagus	oesophagus
22	chr12:83369000-83379000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:83369000-83379000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:83369200-83379400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:83371600-83379600	Weak transcription	Gastric	stomach
26	chr12:83373800-83378200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:83374600-83390000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:83375400-83379600	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:83375600-83405600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:83375800-83377400	Weak transcription	HUVEC	blood vessel
31	chr12:83376000-83381200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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