Variant report

Variant	rs12258025
Chromosome Location	chr10:90661959-90661960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10509558	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10509559	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11202882	0.94[YRI][hapmap];1.00[AMR][1000 genomes]
rs11202884	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs11202885	1.00[AFR][1000 genomes]
rs12240659	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12242274	0.93[YRI][hapmap];0.98[AFR][1000 genomes]
rs12243282	0.94[YRI][hapmap];0.98[AFR][1000 genomes]
rs12243621	0.98[AFR][1000 genomes]
rs12245057	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12245122	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12260182	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs12260572	0.94[YRI][hapmap];0.98[AFR][1000 genomes]
rs12262692	1.00[AMR][1000 genomes]
rs12266049	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs12266993	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114024	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs2231785	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2231786	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3898173	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3898174	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs58014217	1.00[AMR][1000 genomes]
rs58673564	1.00[AFR][1000 genomes]
rs7070713	0.88[YRI][hapmap];1.00[AMR][1000 genomes]
rs73364839	1.00[AFR][1000 genomes]
rs73364841	1.00[AFR][1000 genomes]
rs73364851	1.00[AFR][1000 genomes]
rs9804254	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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:90 , 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	chr10:90652400-90663000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
7	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:90655200-90701400	Weak transcription	Gastric	stomach
9	chr10:90656200-90662000	Enhancers	Primary B cells from peripheral blood	blood
10	chr10:90657400-90664000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr10:90657400-90667800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:90657400-90668000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr10:90657400-90676200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:90657600-90662400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr10:90657600-90670600	Weak transcription	Liver	Liver
16	chr10:90657600-90675400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr10:90657600-90677600	Weak transcription	Lung	lung
18	chr10:90657600-90686400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:90658000-90665000	Weak transcription	Fetal Lung	lung
20	chr10:90658000-90668200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr10:90658000-90672800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:90658400-90665600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:90658600-90686000	Weak transcription	Brain Anterior Caudate	brain
24	chr10:90658800-90664000	Weak transcription	Colonic Mucosa	Colon
25	chr10:90659600-90662000	Enhancers	Fetal Intestine Small	intestine
26	chr10:90659600-90662200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr10:90659600-90689800	Weak transcription	Esophagus	oesophagus
28	chr10:90659800-90662200	Enhancers	Small Intestine	intestine
29	chr10:90659800-90662200	Enhancers	Osteobl	bone
30	chr10:90659800-90665600	Weak transcription	Brain Hippocampus Middle	brain
31	chr10:90660200-90662800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr10:90660400-90662000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr10:90660400-90662000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr10:90660400-90674200	Strong transcription	Primary T cells from cord blood	blood
35	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
36	chr10:90660600-90688200	Strong transcription	Dnd41	blood
37	chr10:90660800-90663200	Genic enhancers	Rectal Mucosa Donor 31	rectum
38	chr10:90661000-90663800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr10:90661000-90666800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr10:90661000-90669400	Strong transcription	Hela-S3	cervix
41	chr10:90661200-90662200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr10:90661200-90663000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr10:90661200-90663600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr10:90661200-90676200	Strong transcription	Fetal Thymus	thymus
45	chr10:90661400-90662000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:90661400-90662000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr10:90661400-90662000	Enhancers	NH-A	brain
48	chr10:90661400-90662200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr10:90661400-90662800	Enhancers	Primary B cells from cord blood	blood
50	chr10:90661400-90663000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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