Variant report

Variant	rs72785019
Chromosome Location	chr16:69892997-69892998
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	chr16:69787646..69790099-chr16:69892380..69895088,2	MCF-7	breast:
2	chr16:69756797..69760411-chr16:69892588..69895419,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC18A-2	chr16:69892891-69893199	l_1356_chr16:69892890-69894263_testes

Variant related genes	Relation type
ENSG00000141101	Chromatin interaction
ENSG00000181019	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11863900	1.00[ASN][1000 genomes]
rs1437137	1.00[ASN][1000 genomes]
rs17298718	1.00[ASN][1000 genomes]
rs17300801	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444781	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45564335	1.00[ASN][1000 genomes]
rs55635123	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55897481	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55921818	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56000913	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127339	1.00[ASN][1000 genomes]
rs56171157	1.00[ASN][1000 genomes]
rs56180453	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56186702	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369384	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377800	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58722949	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499238	1.00[ASN][1000 genomes]
rs689453	1.00[ASN][1000 genomes]
rs689454	1.00[ASN][1000 genomes]
rs689461	1.00[ASN][1000 genomes]
rs7191376	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7203292	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204326	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783105	1.00[ASN][1000 genomes]
rs72783116	1.00[ASN][1000 genomes]
rs72783117	1.00[ASN][1000 genomes]
rs72783118	1.00[ASN][1000 genomes]
rs72783119	1.00[ASN][1000 genomes]
rs72783121	1.00[ASN][1000 genomes]
rs72783128	1.00[ASN][1000 genomes]
rs72783158	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783160	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783163	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783165	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783174	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783183	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783184	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783188	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783189	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783195	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72783198	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785009	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785012	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785020	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785024	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785026	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785029	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785033	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785034	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785037	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785038	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785045	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785047	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785048	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785052	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785055	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785058	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785059	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785064	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785065	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785073	1.00[ASN][1000 genomes]
rs72801347	1.00[ASN][1000 genomes]
rs72801350	1.00[ASN][1000 genomes]
rs72801352	1.00[ASN][1000 genomes]
rs72801354	1.00[ASN][1000 genomes]
rs8055148	1.00[ASN][1000 genomes]
rs8062809	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935643	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	54 gene(s)	inside rSNPs	diseases
2	nsv1062171	chr16:69854267-70188585	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv542941	chr16:69854267-70188585	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1059249	chr16:69854467-70188446	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv542942	chr16:69854467-70188446	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2758428	chr16:69855122-70313222	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2758652	chr16:69855122-70313222	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69834000-69910600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:69837000-69905600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr16:69852000-69893200	Weak transcription	K562	blood
4	chr16:69874000-69905800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr16:69876000-69895000	Weak transcription	Fetal Brain Female	brain
6	chr16:69876000-69904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:69876000-69905800	Weak transcription	Dnd41	blood
8	chr16:69876200-69905800	Weak transcription	Brain Germinal Matrix	brain
9	chr16:69879800-69895000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr16:69882800-69894800	Weak transcription	Colonic Mucosa	Colon
11	chr16:69883000-69893200	Weak transcription	Psoas Muscle	Psoas
12	chr16:69883000-69899400	Weak transcription	NHLF	lung
13	chr16:69883200-69893200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr16:69883200-69894400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr16:69883400-69894800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:69883400-69899600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:69883400-69903800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr16:69883600-69904400	Weak transcription	HMEC	breast
19	chr16:69883800-69895200	Weak transcription	HSMMtube	muscle
20	chr16:69885200-69895600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr16:69885400-69894200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr16:69887400-69894000	Weak transcription	Aorta	Aorta
23	chr16:69887600-69901400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:69887800-69893400	Weak transcription	Brain Anterior Caudate	brain
25	chr16:69887800-69894000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:69887800-69894200	Weak transcription	Brain Angular Gyrus	brain
27	chr16:69888000-69894000	Weak transcription	Esophagus	oesophagus
28	chr16:69888000-69901400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr16:69888000-69905600	Weak transcription	Gastric	stomach
30	chr16:69888200-69893000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr16:69888200-69894200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr16:69888200-69895000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr16:69888200-69895000	Weak transcription	Fetal Stomach	stomach
34	chr16:69888400-69894000	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:69888400-69894200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr16:69888800-69894800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:69889200-69899800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr16:69889600-69905600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr16:69889800-69893000	Weak transcription	Right Ventricle	heart
40	chr16:69889800-69895000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr16:69889800-69895200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr16:69889800-69895400	Weak transcription	NHDF-Ad	bronchial
43	chr16:69890000-69895200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr16:69890400-69923400	Weak transcription	HUVEC	blood vessel
45	chr16:69891000-69898600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr16:69891200-69896800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr16:69891200-69898400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr16:69891600-69898600	Enhancers	Pancreas	Pancrea
49	chr16:69892000-69893200	Enhancers	Placenta	Placenta
50	chr16:69892000-69895200	Strong transcription	Primary B cells from peripheral blood	blood

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