Variant report

Variant	rs12241401
Chromosome Location	chr10:90686071-90686072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1008719	0.95[EUR][1000 genomes]
rs10887870	0.84[EUR][1000 genomes]
rs11202897	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11202898	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202899	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11202902	0.99[EUR][1000 genomes]
rs11202906	0.83[EUR][1000 genomes]
rs11202908	0.90[YRI][hapmap]
rs11591231	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11596205	0.99[EUR][1000 genomes]
rs1214564	0.88[EUR][1000 genomes]
rs12241898	0.84[YRI][hapmap]
rs12254856	0.98[EUR][1000 genomes]
rs12267680	0.98[EUR][1000 genomes]
rs17114327	0.82[EUR][1000 genomes]
rs2119685	0.83[EUR][1000 genomes]
rs2439707	0.86[EUR][1000 genomes]
rs2481918	0.89[EUR][1000 genomes]
rs41284106	0.97[EUR][1000 genomes]
rs41317244	0.98[EUR][1000 genomes]
rs45493098	0.97[EUR][1000 genomes]
rs56104559	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56228317	0.98[EUR][1000 genomes]
rs56268252	0.98[EUR][1000 genomes]
rs57807025	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59737591	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66478243	1.00[AFR][1000 genomes];0.97[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	0.98[EUR][1000 genomes]
rs72809311	0.98[EUR][1000 genomes]
rs72809314	0.98[EUR][1000 genomes]
rs72809318	0.98[EUR][1000 genomes]
rs72809335	0.99[EUR][1000 genomes]
rs72809337	0.97[EUR][1000 genomes]
rs72809342	0.97[EUR][1000 genomes]
rs7897521	0.82[EUR][1000 genomes]
rs7915393	0.83[EUR][1000 genomes]
rs988584	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 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	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
3	chr10:90655200-90701400	Weak transcription	Gastric	stomach
4	chr10:90657600-90686400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:90659600-90689800	Weak transcription	Esophagus	oesophagus
6	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
7	chr10:90660600-90688200	Strong transcription	Dnd41	blood
8	chr10:90661600-90687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr10:90661600-90688800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:90661600-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:90662600-90687600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:90662800-90688800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr10:90664200-90694600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr10:90664400-90691200	Weak transcription	Small Intestine	intestine
15	chr10:90664400-90694800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr10:90666000-90692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr10:90668400-90694800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr10:90669800-90689200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr10:90675800-90696400	Weak transcription	Spleen	Spleen
20	chr10:90677000-90686400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr10:90677800-90687400	Weak transcription	Placenta	Placenta
22	chr10:90678000-90694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr10:90680400-90687400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:90680800-90687000	Strong transcription	Primary B cells from cord blood	blood
25	chr10:90680800-90689200	Strong transcription	Primary T cells from cord blood	blood
26	chr10:90681000-90687600	Strong transcription	Fetal Thymus	thymus
27	chr10:90681000-90688200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:90681200-90687600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:90681200-90688600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr10:90681400-90686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr10:90681400-90687200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:90681400-90697800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr10:90682000-90694800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr10:90683000-90687600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr10:90683000-90688200	Strong transcription	GM12878-XiMat	blood
36	chr10:90683000-90688600	Strong transcription	Fetal Intestine Large	intestine
37	chr10:90683400-90692000	Weak transcription	Hela-S3	cervix
38	chr10:90683600-90686200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr10:90683600-90692200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr10:90683800-90687600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr10:90683800-90694800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:90684400-90686400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr10:90684600-90692200	Weak transcription	Colonic Mucosa	Colon
44	chr10:90684800-90687600	Enhancers	Right Atrium	heart
45	chr10:90684800-90694800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:90685000-90686200	Weak transcription	HSMM	muscle
47	chr10:90685000-90687200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr10:90685000-90692000	Weak transcription	NHEK	skin
49	chr10:90685400-90686600	Enhancers	Fetal Muscle Leg	muscle
50	chr10:90685400-90686800	Enhancers	Fetal Lung	lung

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