Variant report

Variant	rs55742277
Chromosome Location	chr11:58897949-58897950
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	chr11:58896273..58898836-chr11:58901279..58902925,2	K562	blood:

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

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1048374	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229802	0.96[ASN][1000 genomes]
rs11229810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11229832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229835	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229836	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229838	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229841	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229842	1.00[EUR][1000 genomes]
rs11229843	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229844	1.00[EUR][1000 genomes]
rs11229845	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11229847	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12221768	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12222675	1.00[EUR][1000 genomes]
rs12223085	0.82[AFR][1000 genomes]
rs12223473	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225532	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12225972	0.82[AFR][1000 genomes]
rs17153381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2154627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35732637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56349021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57969871	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58277547	0.82[AFR][1000 genomes]
rs60519524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60795438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60883299	0.82[AFR][1000 genomes];1.00[EUR][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:61 , 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	chr11:58886000-58898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:58886600-58898600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:58886800-58898400	Weak transcription	Osteobl	bone
7	chr11:58886800-58898800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:58886800-58901200	Weak transcription	NHLF	lung
9	chr11:58886800-58903400	Weak transcription	NHEK	skin
10	chr11:58887000-58899000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:58887000-58899000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:58888400-58899400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:58891400-58899200	Weak transcription	Left Ventricle	heart
14	chr11:58892200-58899200	Weak transcription	Small Intestine	intestine
15	chr11:58892800-58898000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:58893200-58899000	Weak transcription	Thymus	Thymus
17	chr11:58893400-58898000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:58893600-58898800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:58893600-58898800	Weak transcription	Fetal Thymus	thymus
20	chr11:58893600-58899000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:58893600-58899000	Weak transcription	Fetal Intestine Large	intestine
22	chr11:58893600-58902200	Weak transcription	HSMM	muscle
23	chr11:58893800-58898000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:58893800-58898800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:58893800-58901800	Weak transcription	NHDF-Ad	bronchial
26	chr11:58893800-58903400	Weak transcription	HUVEC	blood vessel
27	chr11:58893800-58909600	Weak transcription	Fetal Brain Male	brain
28	chr11:58894000-58899200	Weak transcription	Adipose Nuclei	Adipose
29	chr11:58894400-58898800	Weak transcription	HMEC	breast
30	chr11:58894400-58899000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:58894600-58898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:58894800-58898800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:58894800-58898800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:58894800-58899000	Weak transcription	Lung	lung
35	chr11:58895000-58898600	Weak transcription	Fetal Lung	lung
36	chr11:58895800-58903400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:58896000-58898200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr11:58896000-58898200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:58896000-58899400	Weak transcription	Aorta	Aorta
40	chr11:58896200-58898000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr11:58896200-58898400	Weak transcription	Liver	Liver
42	chr11:58896200-58899000	Weak transcription	Colonic Mucosa	Colon
43	chr11:58896200-58903200	Strong transcription	Primary T cells from cord blood	blood
44	chr11:58896400-58898200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr11:58896600-58898400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:58896800-58898400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr11:58897000-58898000	Strong transcription	Primary B cells from cord blood	blood
48	chr11:58897000-58898400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:58897000-58899200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:58897200-58900400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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