Variant report

Variant	rs12828809
Chromosome Location	chr12:105016226-105016227
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	chr12:105016224..105018469-chr12:105021634..105023531,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12809841	0.83[TSI][hapmap]
rs12811699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12814462	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12818283	1.00[EUR][1000 genomes]
rs12820999	1.00[CEU][hapmap];1.00[TSI][hapmap]
rs12829137	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12829561	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs34016841	1.00[EUR][1000 genomes]
rs34536312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35904073	0.89[EUR][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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104989400-105030600	Strong transcription	Dnd41	blood
2	chr12:104998800-105031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:104999000-105026800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:105000000-105020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:105000000-105021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:105000400-105019800	Weak transcription	HMEC	breast
7	chr12:105000400-105026000	Weak transcription	NHLF	lung
8	chr12:105003600-105020200	Weak transcription	NHEK	skin
9	chr12:105005800-105019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:105006000-105016400	Weak transcription	A549	lung
11	chr12:105006000-105028200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:105006200-105034800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:105006600-105022600	Weak transcription	Primary B cells from cord blood	blood
14	chr12:105007400-105024400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:105008600-105016400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:105008600-105017600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:105009000-105017000	Weak transcription	Esophagus	oesophagus
18	chr12:105009000-105024400	Weak transcription	Thymus	Thymus
19	chr12:105009400-105017600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:105009400-105019400	Weak transcription	HSMMtube	muscle
21	chr12:105009400-105019600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:105009400-105021200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:105009400-105028200	Weak transcription	Placenta	Placenta
24	chr12:105010000-105017400	Weak transcription	Fetal Brain Female	brain
25	chr12:105010200-105017400	Weak transcription	Fetal Brain Male	brain
26	chr12:105010200-105031600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr12:105010800-105017600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:105011000-105026200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:105012400-105016600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:105013000-105026400	Weak transcription	Fetal Thymus	thymus
31	chr12:105013200-105016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:105013200-105020600	Weak transcription	Aorta	Aorta
33	chr12:105013400-105016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:105013400-105016600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:105013400-105020600	Weak transcription	Right Ventricle	heart
36	chr12:105013600-105016600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:105013800-105016600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:105013800-105016600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr12:105013800-105037000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:105014000-105026400	Weak transcription	Brain Angular Gyrus	brain
41	chr12:105014200-105020800	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:105014600-105016400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:105014800-105017600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:105015000-105016400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:105015000-105016400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:105015000-105017400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:105015000-105017600	Weak transcription	Brain Substantia Nigra	brain
48	chr12:105015000-105017800	Weak transcription	Brain Anterior Caudate	brain
49	chr12:105015000-105019200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:105015200-105016400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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