Variant report

Variant	rs12044039
Chromosome Location	chr1:179310920-179310921
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798665	0.81[ASN][1000 genomes]
rs12022539	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12028643	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12031894	0.82[EUR][1000 genomes]
rs12035050	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039884	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12045521	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12049122	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12049237	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12402165	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12404921	0.82[EUR][1000 genomes]
rs12408668	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13306728	0.83[ASN][1000 genomes]
rs1475798	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16853917	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16853936	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2068234	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2152317	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3753524	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58284152	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60595009	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61821735	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61821737	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61821738	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61821739	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61821740	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61824363	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61824364	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61824365	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61824368	0.83[EUR][1000 genomes]
rs61824371	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61824388	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61824389	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675772	0.82[EUR][1000 genomes]
rs6694339	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7414502	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12044039	TDRD5	cis	Nerve Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179264600-179314000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:179264600-179314000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:179264800-179313800	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:179264800-179313800	Weak transcription	Fetal Brain Female	brain
5	chr1:179264800-179334200	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:179266400-179322800	Weak transcription	Small Intestine	intestine
7	chr1:179268400-179312000	Weak transcription	Fetal Thymus	thymus
8	chr1:179272600-179313800	Weak transcription	Brain Anterior Caudate	brain
9	chr1:179273000-179311600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:179275600-179311600	Weak transcription	HUVEC	blood vessel
11	chr1:179280400-179314000	Weak transcription	NHLF	lung
12	chr1:179282000-179313000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:179282400-179313800	Weak transcription	HSMMtube	muscle
14	chr1:179286400-179313800	Weak transcription	Psoas Muscle	Psoas
15	chr1:179290800-179314000	Weak transcription	NHEK	skin
16	chr1:179292400-179328000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:179293000-179311800	Weak transcription	Fetal Kidney	kidney
18	chr1:179293000-179322600	Weak transcription	Fetal Heart	heart
19	chr1:179293600-179313800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:179293800-179311800	Weak transcription	HMEC	breast
21	chr1:179293800-179314000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:179294200-179324600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:179295600-179314000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:179296800-179327800	Weak transcription	Colonic Mucosa	Colon
25	chr1:179297400-179313600	Weak transcription	Spleen	Spleen
26	chr1:179297400-179321600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:179297800-179311800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:179298600-179311400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:179298600-179324200	Weak transcription	Thymus	Thymus
30	chr1:179299400-179316800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:179299600-179312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:179300200-179313800	Weak transcription	Primary B cells from cord blood	blood
33	chr1:179300200-179314800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:179300400-179334600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:179300600-179322400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:179301800-179322800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:179303000-179314000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:179303200-179324600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:179303400-179322600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:179303600-179311800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:179303600-179314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:179304000-179313800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:179304200-179316000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:179304200-179316600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:179304200-179320000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:179304200-179324400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:179304200-179324400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:179304200-179324600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:179304200-179325200	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr1:179304400-179318400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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