Variant report

Variant	rs73489493
Chromosome Location	chr11:58899379-58899380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPEG1-2	chr11:58897610-58901122	XLOC_009445

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2096585	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2844343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs519287	1.00[AMR][1000 genomes]
rs56963795	1.00[AMR][1000 genomes]
rs58024146	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58355571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58599185	1.00[AMR][1000 genomes]
rs60845282	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61149043	1.00[AMR][1000 genomes]
rs61178453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73474706	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73476916	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73476930	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73476938	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73476939	1.00[AMR][1000 genomes]
rs73483100	1.00[AMR][1000 genomes]
rs73485212	1.00[AMR][1000 genomes]
rs73485235	1.00[AMR][1000 genomes]
rs73487315	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73489468	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73489478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73489480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73489486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73489497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73491310	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73491319	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73491327	0.84[AFR][1000 genomes];1.00[AMR][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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv2757447	chr11:58746238-58906018	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	nsv975329	chr11:58767290-58907813	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv430388	chr11:58769524-58925824	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv468578	chr11:58790628-58901763	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv555147	chr11:58790628-58901763	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv975190	chr11:58893580-58903375	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58875200-58909600	Weak transcription	Stomach Mucosa	stomach
2	chr11:58875400-58909600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:58881600-58903600	Weak transcription	Hela-S3	cervix
4	chr11:58886800-58901200	Weak transcription	NHLF	lung
5	chr11:58886800-58903400	Weak transcription	NHEK	skin
6	chr11:58888400-58899400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr11:58893600-58902200	Weak transcription	HSMM	muscle
8	chr11:58893800-58901800	Weak transcription	NHDF-Ad	bronchial
9	chr11:58893800-58903400	Weak transcription	HUVEC	blood vessel
10	chr11:58893800-58909600	Weak transcription	Fetal Brain Male	brain
11	chr11:58895800-58903400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:58896000-58899400	Weak transcription	Aorta	Aorta
13	chr11:58896200-58903200	Strong transcription	Primary T cells from cord blood	blood
14	chr11:58897200-58900400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:58897200-58901400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr11:58897200-58901800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:58897400-58901400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:58897400-58903600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:58897600-58902800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:58897600-58903200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr11:58897800-58901200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
22	chr11:58897800-58901400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
23	chr11:58898000-58899800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr11:58898000-58899800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:58898000-58900000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr11:58898000-58901000	ZNF genes & repeats	Primary B cells from cord blood	blood
27	chr11:58898000-58902800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr11:58898200-58900000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:58898200-58902000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr11:58898200-58902800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr11:58898400-58900600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr11:58898400-58902800	Strong transcription	Liver	Liver
33	chr11:58898400-58902800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr11:58898600-58900000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
35	chr11:58898600-58900000	Strong transcription	Fetal Lung	lung
36	chr11:58898600-58900200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
37	chr11:58898600-58900400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:58898600-58900400	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:58898600-58901200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr11:58898600-58901400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr11:58898800-58899600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:58898800-58899800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
43	chr11:58898800-58899800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr11:58898800-58900000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:58898800-58900000	ZNF genes & repeats	HMEC	breast
46	chr11:58898800-58900200	ZNF genes & repeats	Fetal Thymus	thymus
47	chr11:58898800-58900400	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr11:58898800-58900600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr11:58898800-58901200	ZNF genes & repeats	Dnd41	blood
50	chr11:58898800-58902800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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