Variant report

Variant	rs2288269
Chromosome Location	chr12:106890151-106890152
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	chr12:106882122..106884058-chr12:106888578..106890580,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10778483	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10778484	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861600	0.85[AMR][1000 genomes]
rs10861607	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10861615	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861616	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11112983	0.83[AMR][1000 genomes]
rs11113012	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11113014	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11113015	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11113016	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11113020	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11113023	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11113025	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12231768	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13561	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17038484	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882413	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs2243506	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs2244958	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2245062	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes]
rs2246353	0.85[AMR][1000 genomes]
rs2249162	0.85[AMR][1000 genomes]
rs2249773	0.85[AMR][1000 genomes]
rs2250262	0.94[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2252685	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2253054	0.81[JPT][hapmap]
rs2254755	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2288266	0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2374609	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34619628	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3851635	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3902141	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137444	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs7137638	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs741624	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3435035	chr12:106765277-107015325	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv832510	chr12:106787730-106951140	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288269	POLR3B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106828600-106905800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:106854400-106904800	Weak transcription	HSMM	muscle
3	chr12:106854600-106899800	Weak transcription	Fetal Thymus	thymus
4	chr12:106855800-106895600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr12:106855800-106896200	Weak transcription	Thymus	Thymus
6	chr12:106856000-106893000	Weak transcription	Right Ventricle	heart
7	chr12:106856800-106899400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:106857200-106890200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:106858600-106895400	Weak transcription	Fetal Heart	heart
10	chr12:106865200-106890600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:106865200-106892400	Weak transcription	Aorta	Aorta
12	chr12:106865400-106890400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:106865400-106890400	Weak transcription	Colonic Mucosa	Colon
14	chr12:106865400-106890400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:106865400-106891800	Weak transcription	Gastric	stomach
16	chr12:106865400-106893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:106865400-106895200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:106865400-106897800	Weak transcription	Spleen	Spleen
19	chr12:106865600-106890200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:106865600-106890200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr12:106865600-106890400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr12:106865600-106890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:106865600-106890400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:106865600-106890400	Weak transcription	Dnd41	blood
26	chr12:106865600-106891000	Weak transcription	Brain Angular Gyrus	brain
27	chr12:106865600-106891200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:106865600-106891400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:106865600-106891400	Weak transcription	Fetal Lung	lung
30	chr12:106865600-106891600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:106865600-106894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:106872200-106891800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:106872600-106897800	Weak transcription	Psoas Muscle	Psoas
34	chr12:106873600-106890400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:106873800-106890800	Weak transcription	Hela-S3	cervix
36	chr12:106874200-106890400	Weak transcription	HSMMtube	muscle
37	chr12:106879800-106890600	Enhancers	Brain Germinal Matrix	brain
38	chr12:106881800-106893000	Weak transcription	K562	blood
39	chr12:106883800-106891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:106884000-106893200	Weak transcription	NH-A	brain
41	chr12:106884400-106891800	Weak transcription	NHEK	skin
42	chr12:106884800-106891400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:106884800-106899800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:106886000-106891800	Weak transcription	HUVEC	blood vessel
45	chr12:106886200-106916400	Weak transcription	A549	lung
46	chr12:106886600-106890800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:106887200-106893400	Weak transcription	Fetal Intestine Large	intestine
48	chr12:106887600-106895400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:106887600-106898000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:106887600-106907800	Weak transcription	Small Intestine	intestine

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