Variant report

Variant	rs3741467
Chromosome Location	chr12:117584066-117584067
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	chr12:117581744..117585061-chr12:117588587..117590635,3	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11068383	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11068398	0.90[ASN][1000 genomes]
rs11068408	0.90[ASN][1000 genomes]
rs11831689	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490118	0.89[ASN][1000 genomes]
rs73206042	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[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	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv899542	chr12:117549739-117623136	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3741467	LOC619208	trans	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117568600-117588400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:117572200-117586400	Weak transcription	NHDF-Ad	bronchial
3	chr12:117572200-117586800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:117572400-117596000	Weak transcription	Fetal Brain Male	brain
5	chr12:117573000-117588400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr12:117578200-117617200	Strong transcription	Fetal Stomach	stomach
7	chr12:117578600-117591400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:117578800-117588400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr12:117578800-117588600	Strong transcription	Fetal Brain Female	brain
10	chr12:117578800-117588600	Weak transcription	Fetal Heart	heart
11	chr12:117579000-117588800	Strong transcription	Brain Germinal Matrix	brain
12	chr12:117579000-117618200	Strong transcription	Thymus	Thymus
13	chr12:117579200-117602600	Weak transcription	Psoas Muscle	Psoas
14	chr12:117579200-117623000	Strong transcription	Primary T cells from cord blood	blood
15	chr12:117579400-117585800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:117579400-117588600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:117579400-117616800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:117579600-117584400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:117579600-117590800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:117579600-117591800	Weak transcription	NH-A	brain
21	chr12:117579800-117585400	Weak transcription	K562	blood
22	chr12:117579800-117585800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:117580000-117584400	Strong transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:117580000-117584400	Strong transcription	Spleen	Spleen
25	chr12:117580000-117593400	Weak transcription	Small Intestine	intestine
26	chr12:117580000-117625000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr12:117580000-117626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:117580200-117584800	Strong transcription	Left Ventricle	heart
29	chr12:117580400-117593600	Weak transcription	HSMM	muscle
30	chr12:117580400-117618800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:117580600-117584600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:117580600-117584800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr12:117580600-117585400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr12:117580600-117588800	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:117580600-117589600	Strong transcription	Dnd41	blood
36	chr12:117580600-117625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:117580800-117584800	Strong transcription	Ovary	ovary
38	chr12:117580800-117588800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:117580800-117589000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:117580800-117590600	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:117581000-117584600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:117581000-117588400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:117581000-117588400	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr12:117581200-117584400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:117581200-117584600	Strong transcription	Right Ventricle	heart
46	chr12:117581200-117584800	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr12:117581200-117588600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:117581200-117588600	Strong transcription	Primary hematopoietic stem cells	blood
49	chr12:117581200-117618400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:117581200-117624600	Strong transcription	Duodenum Mucosa	Duodenum

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