Variant report

Variant	rs41317244
Chromosome Location	chr10:90653631-90653632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIPM-1	chr10:90653628-90653670	NONHSAT015480

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

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1008719	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	0.96[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	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41284106	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45493098	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56104559	0.99[EUR][1000 genomes]
rs56228317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56268252	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	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809318	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	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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
2	chr10:90641800-90653800	Weak transcription	Stomach Mucosa	stomach
3	chr10:90641800-90656400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
5	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:90642200-90656600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:90642600-90653800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr10:90642800-90656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:90646800-90656200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:90646800-90656800	Weak transcription	Psoas Muscle	Psoas
12	chr10:90647400-90656000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
14	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
15	chr10:90648000-90654200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr10:90648000-90656000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:90648200-90654000	Weak transcription	Fetal Thymus	thymus
18	chr10:90648200-90654800	Weak transcription	Left Ventricle	heart
19	chr10:90648400-90656200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:90649800-90654200	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr10:90649800-90654200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:90650000-90656200	Weak transcription	Fetal Stomach	stomach
23	chr10:90650200-90654200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:90650400-90653800	Enhancers	HSMM	muscle
25	chr10:90650800-90656400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr10:90651000-90655000	Enhancers	A549	lung
27	chr10:90651600-90654400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr10:90651600-90656000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr10:90651800-90655200	Enhancers	Small Intestine	intestine
30	chr10:90652000-90658200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr10:90652200-90654400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr10:90652200-90656000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr10:90652400-90653800	Weak transcription	Dnd41	blood
34	chr10:90652400-90654800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:90652400-90655800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr10:90652400-90656200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr10:90652400-90656200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr10:90652400-90656200	Weak transcription	Ovary	ovary
39	chr10:90652400-90656400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr10:90652400-90656600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr10:90652400-90656600	Weak transcription	HSMMtube	muscle
42	chr10:90652400-90656800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr10:90652400-90663000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:90652600-90653800	Weak transcription	GM12878-XiMat	blood
45	chr10:90652600-90656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr10:90652600-90656600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:90652600-90656600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr10:90652600-90656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr10:90652600-90656800	Weak transcription	NH-A	brain
50	chr10:90652600-90657000	Weak transcription	Brain Substantia Nigra	brain

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