Variant report

Variant	rs57093304
Chromosome Location	chr1:95527446-95527447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM56-2	chr1:95527152-95527745	ENSG00000230427.1

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs41292697	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56032536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56204307	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs57040913	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57122039	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57213707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57950891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59130528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59338711	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59569067	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60405904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60491236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60549805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60555923	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60757816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61488063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61772226	1.00[AFR][1000 genomes]
rs61774271	1.00[AFR][1000 genomes]
rs74101957	0.81[EUR][1000 genomes]
rs74101958	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74101961	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74101968	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74101972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74101979	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101983	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101989	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101991	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101993	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101995	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101998	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74101999	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74102002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103604	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103606	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74103644	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74103651	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs74103654	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3402740	chr1:95500980-95527860	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95488200-95537600	Weak transcription	Right Ventricle	heart
2	chr1:95491600-95529600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:95505600-95537400	Weak transcription	Right Atrium	heart
4	chr1:95506000-95537800	Weak transcription	Pancreas	Pancrea
5	chr1:95506600-95527800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:95509000-95528000	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:95509400-95527600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:95509400-95532800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:95509400-95534200	Weak transcription	Fetal Intestine Small	intestine
10	chr1:95514400-95527800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:95514600-95530200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:95515600-95535800	Weak transcription	Fetal Lung	lung
13	chr1:95516000-95537200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:95516200-95532600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:95517000-95528000	Weak transcription	Liver	Liver
16	chr1:95517400-95537800	Weak transcription	Esophagus	oesophagus
17	chr1:95518000-95537000	Weak transcription	Psoas Muscle	Psoas
18	chr1:95518000-95537200	Weak transcription	HSMM	muscle
19	chr1:95518400-95529400	Weak transcription	Ovary	ovary
20	chr1:95521600-95537400	Weak transcription	Brain Germinal Matrix	brain
21	chr1:95523200-95527600	Weak transcription	Fetal Brain Female	brain
22	chr1:95523200-95537600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:95523400-95532600	Weak transcription	Brain Angular Gyrus	brain
24	chr1:95523400-95537800	Weak transcription	Left Ventricle	heart
25	chr1:95523600-95528800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:95523600-95530200	Weak transcription	Fetal Intestine Large	intestine
27	chr1:95523600-95531200	Weak transcription	Lung	lung
28	chr1:95523600-95534400	Weak transcription	Small Intestine	intestine
29	chr1:95523600-95537200	Weak transcription	NHLF	lung
30	chr1:95523800-95537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:95523800-95537200	Weak transcription	HSMMtube	muscle
32	chr1:95523800-95537800	Weak transcription	Fetal Thymus	thymus
33	chr1:95524000-95528400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:95524000-95529400	Weak transcription	Dnd41	blood
35	chr1:95524000-95537200	Weak transcription	NH-A	brain
36	chr1:95524400-95528000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:95524400-95528000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:95524400-95528800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:95524400-95529000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:95524400-95534600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:95524400-95537200	Weak transcription	Osteobl	bone
42	chr1:95524600-95529600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr1:95524600-95532800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:95524600-95537400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr1:95524600-95537600	Weak transcription	Colonic Mucosa	Colon
46	chr1:95524600-95537600	Weak transcription	Placenta	Placenta
47	chr1:95524800-95528800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:95525000-95537200	Weak transcription	Primary B cells from cord blood	blood
49	chr1:95525000-95537400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:95525200-95527800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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