Variant report

Variant	rs28454254
Chromosome Location	chr10:50675598-50675599
allele	A/G
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:37)

rs_ID	r²[population]
rs10776576	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10857494	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857495	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857496	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857498	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857500	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11101133	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11101137	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101140	0.82[AMR][1000 genomes]
rs11101152	0.83[ASN][1000 genomes]
rs11527805	0.82[ASN][1000 genomes]
rs12219170	0.83[ASN][1000 genomes]
rs12219670	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12220085	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12221460	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12244804	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1924488	0.82[AMR][1000 genomes]
rs2228528	0.82[AMR][1000 genomes]
rs2281794	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750748	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750749	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4253004	0.83[ASN][1000 genomes]
rs4253013	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253040	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253043	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4253060	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4253095	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4253138	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4253145	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4253215	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61143747	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7080607	0.87[AFR][1000 genomes]
rs7086144	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73297748	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73305562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909342	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv895377	chr10:50588990-50678212	ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
6	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv1051636	chr10:50675292-50732280	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50662200-50677800	Weak transcription	Fetal Heart	heart
2	chr10:50662200-50691600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:50662400-50690000	Weak transcription	Stomach Mucosa	stomach
4	chr10:50662400-50693200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:50662600-50676600	Weak transcription	Small Intestine	intestine
6	chr10:50662600-50677600	Weak transcription	NHDF-Ad	bronchial
7	chr10:50662600-50691400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr10:50663000-50675800	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:50663200-50693800	Weak transcription	HepG2	liver
10	chr10:50664000-50677400	Weak transcription	Fetal Kidney	kidney
11	chr10:50664600-50678200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr10:50666600-50676400	Weak transcription	K562	blood
13	chr10:50666600-50684400	Weak transcription	NHLF	lung
14	chr10:50666800-50678200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr10:50667600-50675600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr10:50667800-50677600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr10:50667800-50707400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:50668000-50713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr10:50668200-50675800	Weak transcription	Esophagus	oesophagus
20	chr10:50668200-50680200	Weak transcription	GM12878-XiMat	blood
21	chr10:50668400-50676400	Weak transcription	Hela-S3	cervix
22	chr10:50668400-50677600	Weak transcription	NH-A	brain
23	chr10:50668400-50677800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:50668400-50677800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr10:50668400-50678200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr10:50668800-50677600	Weak transcription	Psoas Muscle	Psoas
27	chr10:50668800-50677800	Weak transcription	Fetal Thymus	thymus
28	chr10:50669000-50678200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr10:50669600-50675600	Weak transcription	Fetal Intestine Large	intestine
30	chr10:50669600-50675600	Weak transcription	Gastric	stomach
31	chr10:50669600-50675800	Weak transcription	Brain Anterior Caudate	brain
32	chr10:50669600-50675800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr10:50669600-50675800	Weak transcription	Spleen	Spleen
34	chr10:50669600-50676000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:50669600-50676000	Weak transcription	Brain Angular Gyrus	brain
36	chr10:50669600-50676000	Weak transcription	Brain Substantia Nigra	brain
37	chr10:50669600-50676000	Weak transcription	Fetal Brain Female	brain
38	chr10:50669600-50676000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr10:50669600-50676000	Weak transcription	Right Ventricle	heart
40	chr10:50669600-50676200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr10:50669600-50677800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:50670600-50691600	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr10:50671600-50686600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:50671800-50679400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr10:50671800-50693800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr10:50672000-50679600	Weak transcription	Dnd41	blood
47	chr10:50672000-50687200	Strong transcription	Fetal Muscle Leg	muscle
48	chr10:50672000-50691800	Strong transcription	Primary T cells from cord blood	blood
49	chr10:50672200-50676000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr10:50672200-50679400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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