Variant report

Variant	rs56228317
Chromosome Location	chr10:90663452-90663453
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:40)

rs_ID	r²[population]
rs1008719	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10887870	0.84[EUR][1000 genomes]
rs11202897	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202898	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202899	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202901	0.80[AMR][1000 genomes]
rs11202902	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202906	0.83[EUR][1000 genomes]
rs11591231	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11596205	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1214564	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12241401	0.98[EUR][1000 genomes]
rs12254856	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12267680	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17114327	0.82[EUR][1000 genomes]
rs2119685	0.83[EUR][1000 genomes]
rs2439707	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2481918	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41284106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41317244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45493098	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56104559	0.99[EUR][1000 genomes]
rs56268252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57807025	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59737591	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66478243	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7078383	0.82[EUR][1000 genomes]
rs7085698	0.84[EUR][1000 genomes]
rs7090631	0.84[EUR][1000 genomes]
rs7098235	0.84[EUR][1000 genomes]
rs72809310	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809314	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809335	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809337	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72809342	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7897521	0.82[EUR][1000 genomes]
rs7915393	0.83[EUR][1000 genomes]
rs988584	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
4	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
5	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
6	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:90655200-90701400	Weak transcription	Gastric	stomach
8	chr10:90657400-90664000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:90657400-90667800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:90657400-90668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:90657400-90676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr10:90657600-90670600	Weak transcription	Liver	Liver
13	chr10:90657600-90675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:90657600-90677600	Weak transcription	Lung	lung
15	chr10:90657600-90686400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:90658000-90665000	Weak transcription	Fetal Lung	lung
17	chr10:90658000-90668200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:90658000-90672800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr10:90658400-90665600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:90658600-90686000	Weak transcription	Brain Anterior Caudate	brain
21	chr10:90658800-90664000	Weak transcription	Colonic Mucosa	Colon
22	chr10:90659600-90689800	Weak transcription	Esophagus	oesophagus
23	chr10:90659800-90665600	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:90660400-90674200	Strong transcription	Primary T cells from cord blood	blood
25	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
26	chr10:90660600-90688200	Strong transcription	Dnd41	blood
27	chr10:90661000-90663800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr10:90661000-90666800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr10:90661000-90669400	Strong transcription	Hela-S3	cervix
30	chr10:90661200-90663600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr10:90661200-90676200	Strong transcription	Fetal Thymus	thymus
32	chr10:90661400-90667400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:90661400-90667400	Strong transcription	A549	lung
34	chr10:90661400-90669000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr10:90661600-90678400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr10:90661600-90687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr10:90661600-90688800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr10:90661600-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:90661800-90664400	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr10:90661800-90664600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr10:90661800-90665000	Genic enhancers	Fetal Intestine Large	intestine
42	chr10:90661800-90665800	Strong transcription	Fetal Muscle Leg	muscle
43	chr10:90661800-90674200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr10:90662000-90663800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:90662000-90667800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:90662000-90676200	Weak transcription	NH-A	brain
47	chr10:90662000-90683000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:90662200-90663800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr10:90662200-90663800	Strong transcription	NHLF	lung
50	chr10:90662200-90664000	Weak transcription	Small Intestine	intestine

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