Variant report

Variant	rs12428055
Chromosome Location	chr13:48645889-48645890
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	chr13:48638983..48640532-chr13:48645764..48648632,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11838539	0.86[EUR][1000 genomes]
rs12427516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427964	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12428102	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12429099	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429105	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12429348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429993	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12430076	0.85[AMR][1000 genomes]
rs12430172	0.85[AMR][1000 genomes]
rs12431057	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12431130	0.86[EUR][1000 genomes]
rs1968029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148242	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182374	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2182375	0.82[ASN][1000 genomes]
rs2182377	0.82[ASN][1000 genomes]
rs2897496	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35710390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57698455	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57957392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58634823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61585711	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002322	0.82[ASN][1000 genomes]
rs840430	0.82[ASN][1000 genomes]
rs9534910	0.82[ASN][1000 genomes]
rs9534936	0.93[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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr13:48623200-48652200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:48636600-48651400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:48636600-48655400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:48638200-48650000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr13:48638800-48651400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr13:48638800-48651600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:48639000-48648800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:48639400-48648600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
10	chr13:48639600-48649800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr13:48640000-48648600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
12	chr13:48640000-48649800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr13:48640200-48646600	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr13:48640200-48647000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
15	chr13:48640200-48648600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:48640200-48648600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
17	chr13:48640200-48648600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:48640200-48648600	ZNF genes & repeats	Fetal Brain Female	brain
19	chr13:48640200-48648600	ZNF genes & repeats	Fetal Lung	lung
20	chr13:48640200-48648600	ZNF genes & repeats	Fetal Muscle Leg	muscle
21	chr13:48640200-48649800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:48640200-48649800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr13:48640200-48649800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr13:48640200-48661200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr13:48640400-48648200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr13:48640400-48648600	ZNF genes & repeats	Liver	Liver
27	chr13:48640400-48655600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:48640600-48648400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:48640800-48647000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr13:48640800-48648200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr13:48640800-48648600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
32	chr13:48641200-48647400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:48641600-48647400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
34	chr13:48641600-48647600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr13:48641600-48648800	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr13:48641800-48647000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr13:48641800-48647400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr13:48641800-48648200	ZNF genes & repeats	NHEK	skin
39	chr13:48642000-48646400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr13:48642000-48646400	Weak transcription	K562	blood
41	chr13:48642200-48646600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr13:48642400-48648400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr13:48642600-48646000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
44	chr13:48642600-48650200	ZNF genes & repeats	Dnd41	blood
45	chr13:48642600-48653800	Strong transcription	Brain Angular Gyrus	brain
46	chr13:48642800-48646200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr13:48642800-48646400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
48	chr13:48642800-48653800	Strong transcription	A549	lung
49	chr13:48643000-48646000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:48643000-48646600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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