Variant report

Variant	rs17153379
Chromosome Location	chr11:58901552-58901553
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:58892733..58893477-chr11:58901491..58902182,2	K562	blood:
2	chr11:58896273..58898836-chr11:58901279..58902925,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPEG1-2	chr11:58901132-58902156	XLOC_009445
2	lnc-MPEG1-2	chr11:58901446-58903061	NR_110184

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10128559	0.92[ASN][1000 genomes]
rs10128605	0.80[EUR][1000 genomes]
rs10128661	0.88[EUR][1000 genomes]
rs10437720	0.89[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs10792211	0.88[YRI][hapmap]
rs10792219	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10792221	0.94[EUR][1000 genomes]
rs10896914	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10896922	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896924	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896925	0.89[CEU][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs10896926	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896928	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs10896929	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10896930	0.94[EUR][1000 genomes]
rs10896931	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes]
rs10896932	0.90[CHB][hapmap];0.94[EUR][1000 genomes]
rs10896933	0.93[EUR][1000 genomes]
rs10896934	0.86[EUR][1000 genomes]
rs10896935	0.84[EUR][1000 genomes]
rs10896936	0.93[EUR][1000 genomes]
rs10896937	0.93[EUR][1000 genomes]
rs10896938	0.85[EUR][1000 genomes]
rs10896947	0.89[CEU][hapmap]
rs11229795	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11229798	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229799	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229801	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229837	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11229840	0.89[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs11229848	0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs11229849	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs11229850	1.00[CHB][hapmap]
rs11229851	0.94[EUR][1000 genomes]
rs11229852	0.94[EUR][1000 genomes]
rs11229854	0.94[EUR][1000 genomes]
rs11229856	0.93[EUR][1000 genomes]
rs11823977	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825017	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271831	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs12272113	0.94[EUR][1000 genomes]
rs12274008	1.00[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs12275487	1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs12278163	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12280068	1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs12283633	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12290612	0.90[YRI][hapmap]
rs12292185	0.91[EUR][1000 genomes]
rs12292779	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs12293649	1.00[CHB][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs12293695	0.94[EUR][1000 genomes]
rs12362905	0.94[EUR][1000 genomes]
rs12802129	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17153383	0.97[EUR][1000 genomes]
rs17153415	0.90[EUR][1000 genomes]
rs1938588	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938589	0.97[EUR][1000 genomes]
rs1938781	0.89[CEU][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs1943146	0.89[ASN][1000 genomes]
rs1943147	0.89[ASN][1000 genomes]
rs2096544	0.94[EUR][1000 genomes]
rs2096586	0.88[EUR][1000 genomes]
rs2096587	0.91[EUR][1000 genomes]
rs2105506	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2105507	0.94[EUR][1000 genomes]
rs2154628	0.86[EUR][1000 genomes]
rs2186380	0.94[EUR][1000 genomes]
rs2282482	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282483	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2839968	0.89[CEU][hapmap]
rs2844342	0.90[ASN][1000 genomes]
rs2849739	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34027305	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34239454	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34501069	0.94[EUR][1000 genomes]
rs35293773	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3802961	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474847	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs530386	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs55657403	0.87[EUR][1000 genomes]
rs55689653	0.94[EUR][1000 genomes]
rs55989038	0.86[EUR][1000 genomes]
rs56137001	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56239606	0.86[EUR][1000 genomes]
rs58722008	0.89[EUR][1000 genomes]
rs61902181	0.94[EUR][1000 genomes]
rs61902223	0.94[EUR][1000 genomes]
rs7126078	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7933787	0.89[CEU][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs7950880	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	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:101 , 50 per page) page: 1 2 3

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	chr11:58886800-58903400	Weak transcription	NHEK	skin
5	chr11:58893600-58902200	Weak transcription	HSMM	muscle
6	chr11:58893800-58901800	Weak transcription	NHDF-Ad	bronchial
7	chr11:58893800-58903400	Weak transcription	HUVEC	blood vessel
8	chr11:58893800-58909600	Weak transcription	Fetal Brain Male	brain
9	chr11:58895800-58903400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:58896200-58903200	Strong transcription	Primary T cells from cord blood	blood
11	chr11:58897200-58901800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:58897400-58903600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr11:58897600-58902800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:58897600-58903200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:58898000-58902800	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:58898200-58902000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:58898200-58902800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr11:58898400-58902800	Strong transcription	Liver	Liver
19	chr11:58898400-58902800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:58898800-58902800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:58899000-58902400	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:58899000-58909600	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:58899200-58903200	Weak transcription	Pancreas	Pancrea
24	chr11:58899200-58903200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:58899400-58903400	Weak transcription	Fetal Kidney	kidney
26	chr11:58899600-58903200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr11:58899600-58903400	Weak transcription	Brain Anterior Caudate	brain
28	chr11:58899600-58903400	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:58899600-58903600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr11:58899600-58903600	Weak transcription	Esophagus	oesophagus
31	chr11:58899600-58909600	Weak transcription	Aorta	Aorta
32	chr11:58899800-58902400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:58899800-58902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr11:58899800-58903000	Strong transcription	Fetal Intestine Large	intestine
35	chr11:58899800-58903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:58899800-58903200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr11:58899800-58903200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:58899800-58903200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:58899800-58903200	Weak transcription	Fetal Muscle Leg	muscle
40	chr11:58899800-58903200	Weak transcription	Fetal Stomach	stomach
41	chr11:58899800-58903400	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:58899800-58903400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:58899800-58903400	Weak transcription	Placenta	Placenta
44	chr11:58899800-58903400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr11:58899800-58904800	Weak transcription	Left Ventricle	heart
46	chr11:58899800-58909600	Weak transcription	Colonic Mucosa	Colon
47	chr11:58899800-58909800	Weak transcription	Gastric	stomach
48	chr11:58899800-58909800	Weak transcription	Small Intestine	intestine
49	chr11:58899800-58910000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:58900000-58901600	Weak transcription	Ovary	ovary

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