Variant report

Variant	rs10054480
Chromosome Location	chr5:99874553-99874554
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10043796	1.00[ASN][1000 genomes]
rs10044020	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053309	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054650	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17447375	1.00[YRI][hapmap]
rs17447382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774525	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036562	1.00[ASN][1000 genomes]
rs34462099	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550123	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068466	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3911547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55825520	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55895019	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68104976	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6869843	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871027	0.87[ASN][1000 genomes]
rs6872159	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6874840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879886	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890035	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892505	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898051	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72774688	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714303	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9327206	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759359	chr5:99207674-99883371	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv2757124	chr5:99424756-99883371	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1025132	chr5:99745775-99896429	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99871800-99886400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:99871800-99886400	Weak transcription	Lung	lung
3	chr5:99871800-99886800	Weak transcription	Pancreas	Pancrea
4	chr5:99871800-99889400	Weak transcription	Spleen	Spleen
5	chr5:99871800-99890200	Weak transcription	Gastric	stomach
6	chr5:99872000-99875000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr5:99872000-99881800	Weak transcription	Left Ventricle	heart
8	chr5:99872200-99875000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr5:99872400-99874600	Enhancers	Rectal Smooth Muscle	rectum
10	chr5:99872400-99874800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr5:99872400-99875000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:99872400-99875800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:99872400-99876600	Weak transcription	Esophagus	oesophagus
14	chr5:99872400-99886200	Weak transcription	Small Intestine	intestine
15	chr5:99872400-99931400	Weak transcription	Aorta	Aorta
16	chr5:99872600-99881800	Weak transcription	Right Atrium	heart
17	chr5:99872600-99886400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:99872600-99922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:99872800-99874800	Weak transcription	HMEC	breast
20	chr5:99872800-99875200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr5:99872800-99876400	Weak transcription	Psoas Muscle	Psoas
22	chr5:99872800-99879600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:99872800-99886200	Weak transcription	HSMMtube	muscle
24	chr5:99872800-99886200	Weak transcription	Osteobl	bone
25	chr5:99872800-99886400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:99872800-99902000	Weak transcription	HSMM	muscle
27	chr5:99872800-99916200	Weak transcription	Ovary	ovary
28	chr5:99873000-99875000	Active TSS	GM12878-XiMat	blood
29	chr5:99873000-99876000	Weak transcription	Fetal Heart	heart
30	chr5:99873000-99877600	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:99873000-99879400	Weak transcription	Primary B cells from cord blood	blood
32	chr5:99873000-99886400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr5:99873400-99874600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr5:99873400-99875200	Weak transcription	Hela-S3	cervix
35	chr5:99873400-99881800	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:99873400-99882000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:99873400-99897000	Weak transcription	Primary T cells from cord blood	blood
38	chr5:99873400-99916200	Weak transcription	Fetal Stomach	stomach
39	chr5:99873400-99930600	Weak transcription	NH-A	brain
40	chr5:99873600-99874600	Enhancers	Brain Angular Gyrus	brain
41	chr5:99873600-99874600	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:99873600-99883800	Weak transcription	Brain Germinal Matrix	brain
43	chr5:99873800-99876600	Weak transcription	NHDF-Ad	bronchial
44	chr5:99873800-99877600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:99873800-99886400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:99874000-99874800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:99874000-99876000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:99874000-99877200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:99874000-99886200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:99874000-99897800	Weak transcription	Adipose Nuclei	Adipose

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