Variant report

Variant	rs9403380
Chromosome Location	chr6:142652416-142652417
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142650601..142652419-chr6:142665853..142668621,2	MCF-7	breast:
2	chr6:142624264..142626987-chr6:142649609..142652476,2	MCF-7	breast:
3	chr6:142619918..142621591-chr6:142650811..142653503,2	MCF-7	breast:
4	chr6:142644240..142648928-chr6:142651290..142656139,5	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1040525	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1040526	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1342060	0.93[EUR][1000 genomes]
rs1360194	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1418201	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155259	0.81[EUR][1000 genomes]
rs1891308	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039986	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2039987	0.94[EUR][1000 genomes]
rs2050157	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294764	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294771	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs262119	0.81[EUR][1000 genomes]
rs262121	0.81[EUR][1000 genomes]
rs262129	0.81[EUR][1000 genomes]
rs263180	0.81[EUR][1000 genomes]
rs263181	0.81[EUR][1000 genomes]
rs263182	0.81[EUR][1000 genomes]
rs263183	0.81[EUR][1000 genomes]
rs263184	0.81[EUR][1000 genomes]
rs263186	0.81[EUR][1000 genomes]
rs263187	0.81[EUR][1000 genomes]
rs263188	0.81[EUR][1000 genomes]
rs263189	0.81[EUR][1000 genomes]
rs3748069	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3817929	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4896582	0.86[EUR][1000 genomes]
rs6570507	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570508	0.85[EUR][1000 genomes]
rs6570509	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570510	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6909857	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6929442	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6937121	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741741	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7754638	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7755109	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7756305	0.93[EUR][1000 genomes]
rs7763064	0.85[EUR][1000 genomes]
rs7770386	0.89[EUR][1000 genomes]
rs7774095	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776375	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9373346	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9389984	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9389985	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9389986	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9389987	0.91[EUR][1000 genomes]
rs9399401	0.93[EUR][1000 genomes]
rs9403381	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9403382	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403383	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9403387	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9496346	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9496369	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9496374	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9496392	0.86[EUR][1000 genomes]
rs962554	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs972982	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142643000-142653800	Weak transcription	Fetal Heart	heart
2	chr6:142646000-142652600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:142649000-142655400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:142649800-142653800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:142650600-142653600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:142650600-142654200	Enhancers	HMEC	breast
7	chr6:142650800-142652600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:142650800-142654200	Enhancers	Fetal Lung	lung
9	chr6:142650800-142654600	Enhancers	NHLF	lung
10	chr6:142651000-142652600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:142651000-142653200	Enhancers	NHEK	skin
12	chr6:142651000-142654600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:142651000-142656600	Enhancers	Liver	Liver
14	chr6:142651200-142652600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:142651200-142653000	Enhancers	Fetal Thymus	thymus
16	chr6:142651200-142654400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:142651400-142654800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:142651600-142653200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:142651800-142652600	Enhancers	HSMM	muscle
20	chr6:142651800-142653400	Enhancers	Primary T cells from cord blood	blood
21	chr6:142651800-142654000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:142652000-142652600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:142652000-142652600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:142652000-142653000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:142652000-142653000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:142652000-142653200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:142652000-142653200	Enhancers	Dnd41	blood
28	chr6:142652200-142652600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr6:142652200-142652600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:142652200-142652600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:142652200-142652600	Enhancers	Fetal Intestine Small	intestine
32	chr6:142652200-142652600	Enhancers	Fetal Stomach	stomach
33	chr6:142652200-142652600	Enhancers	NH-A	brain
34	chr6:142652200-142652800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr6:142652200-142653000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:142652200-142653000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr6:142652200-142653000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:142652200-142653200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr6:142652200-142653800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:142652400-142652600	Enhancers	Esophagus	oesophagus
41	chr6:142652400-142652600	Flanking Active TSS	A549	lung
42	chr6:142652400-142652800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:142652400-142653000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:142652400-142653000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr6:142652400-142653000	Flanking Active TSS	HUVEC	blood vessel
46	chr6:142652400-142653200	Flanking Active TSS	HepG2	liver
47	chr6:142652400-142654200	Enhancers	Primary hematopoietic stem cells	blood

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