Variant report

Variant	rs28371425
Chromosome Location	chr14:71608711-71608712
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	chr14:71608562..71610263-chr14:71786915..71789760,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K9-10	chr14:71607842-71609970	ENSG00000269927.1

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10133733	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10139448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10142792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10145022	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10147124	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11846003	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11847244	0.83[EUR][1000 genomes]
rs11849831	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12432180	0.83[EUR][1000 genomes]
rs12432587	0.81[ASN][1000 genomes]
rs12433409	0.83[EUR][1000 genomes]
rs12436649	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12436920	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12436970	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12436976	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12880918	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12884923	0.92[ASN][1000 genomes]
rs12886096	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12891140	0.83[EUR][1000 genomes]
rs12891445	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17108753	0.81[EUR][1000 genomes]
rs17108869	0.83[EUR][1000 genomes]
rs17108873	0.83[EUR][1000 genomes]
rs17108897	0.83[EUR][1000 genomes]
rs17109008	0.85[ASN][1000 genomes]
rs1978163	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2051865	0.83[EUR][1000 genomes]
rs2158998	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286312	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2286314	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2526891	0.83[EUR][1000 genomes]
rs34007279	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34740221	0.83[EUR][1000 genomes]
rs34927411	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34971726	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34998980	0.83[EUR][1000 genomes]
rs35041597	0.83[EUR][1000 genomes]
rs35092982	0.83[EUR][1000 genomes]
rs35523654	0.83[EUR][1000 genomes]
rs35714454	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36089307	0.83[EUR][1000 genomes]
rs4488390	0.83[EUR][1000 genomes]
rs4614662	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4902872	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4902877	0.83[EUR][1000 genomes]
rs4902878	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4902882	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4902883	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902884	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71425229	0.83[EUR][1000 genomes]
rs7147788	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7148530	0.81[ASN][1000 genomes]
rs7152435	0.81[ASN][1000 genomes]
rs7157279	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7158548	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73297555	0.83[ASN][1000 genomes]
rs8010701	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8015773	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9989203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1037839	chr14:71263886-71625114	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv542127	chr14:71263886-71625114	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv565043	chr14:71395604-71625112	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71605600-71613200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr14:71605600-71613400	Enhancers	Placenta	Placenta
3	chr14:71605800-71608800	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr14:71605800-71608800	Weak transcription	HUVEC	blood vessel
5	chr14:71605800-71609400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr14:71606000-71608800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr14:71606000-71609000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:71606000-71610000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr14:71606000-71610000	Weak transcription	Stomach Mucosa	stomach
10	chr14:71606200-71608800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:71606200-71608800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr14:71606200-71609000	Weak transcription	K562	blood
13	chr14:71606200-71609200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:71606200-71609400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:71606200-71609400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:71606200-71610000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr14:71606200-71610000	Weak transcription	Brain Anterior Caudate	brain
18	chr14:71606200-71610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr14:71606200-71610800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr14:71606400-71609800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr14:71606400-71610000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr14:71606400-71610200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:71606400-71610200	Weak transcription	Adipose Nuclei	Adipose
24	chr14:71606400-71610200	Weak transcription	Liver	Liver
25	chr14:71606600-71610200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr14:71606600-71610200	Weak transcription	HSMMtube	muscle
27	chr14:71606600-71614800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr14:71607200-71610800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr14:71607400-71609000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:71607400-71610000	Weak transcription	Fetal Intestine Large	intestine
31	chr14:71607600-71610800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr14:71607800-71610800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:71607800-71610800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:71607800-71610800	Enhancers	NHDF-Ad	bronchial
35	chr14:71608000-71611200	Enhancers	Primary B cells from cord blood	blood
36	chr14:71608200-71610200	Enhancers	Primary B cells from peripheral blood	blood
37	chr14:71608200-71610800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr14:71608200-71610800	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr14:71608200-71610800	Enhancers	Osteobl	bone
40	chr14:71608400-71609000	Flanking Active TSS	NH-A	brain
41	chr14:71608400-71609200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:71608400-71609200	Enhancers	Spleen	Spleen
43	chr14:71608400-71609400	Enhancers	Hela-S3	cervix
44	chr14:71608400-71610400	Enhancers	Primary hematopoietic stem cells	blood
45	chr14:71608400-71610600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr14:71608400-71610600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:71608400-71610800	Enhancers	Primary T cells from cord blood	blood
48	chr14:71608400-71610800	Enhancers	Muscle Satellite Cultured Cells	--
49	chr14:71608400-71610800	Enhancers	HepG2	liver
50	chr14:71608400-71610800	Enhancers	HMEC	breast

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