Variant report

Variant	rs1113389
Chromosome Location	chr2:172635365-172635366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10166005	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10167419	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174525	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184866	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10194102	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10200608	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10201419	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10204502	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10204622	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206062	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10207085	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10432423	0.80[EUR][1000 genomes]
rs10497374	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10803863	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11678984	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11757	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886820	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11897196	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11904009	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12053003	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12185567	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692970	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12692973	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692974	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12692978	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13017585	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13018768	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13022113	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13419987	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429113	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13429409	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1474074	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554166	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1973706	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292815	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357061	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2674484	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2678155	0.91[AMR][1000 genomes]
rs312916	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312918	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs312919	0.83[AMR][1000 genomes]
rs312921	0.83[EUR][1000 genomes]
rs312924	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs312925	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34358700	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34542126	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35379278	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35391289	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35549875	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35645520	0.82[AMR][1000 genomes]
rs35854280	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36057702	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770451	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770452	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795999	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4667693	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4667694	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4668412	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4668414	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433311	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433314	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66835971	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705200	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709156	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710698	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67204065	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721680	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6722757	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6724337	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6725388	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6738445	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745143	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754817	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757773	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6758704	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759575	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71013062	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7355523	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7355594	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562356	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7572215	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7573003	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7586207	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597387	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7604918	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7608403	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs908670	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs908671	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973889	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1113389	AC068039.4	cis	Nerve Tibial	GTEx
rs1113389	AC068039.4	cis	lung	GTEx
rs1113389	AC068039.4	cis	Heart Left Ventricle	GTEx
rs1113389	AC068039.4	cis	Esophagus Mucosa	GTEx
rs1113389	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs1113389	AC068039.4	cis	Thyroid	GTEx
rs1113389	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs1113389	AC068039.4	cis	Stomach	GTEx
rs1113389	AC068039.4	cis	Esophagus Muscularis	GTEx
rs1113389	AC068039.4	cis	Whole Blood	GTEx
rs1113389	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs1113389	AC068039.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
2	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr2:172604400-172641200	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:172618000-172639600	Weak transcription	Fetal Heart	heart
7	chr2:172618400-172639800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr2:172618400-172641000	Weak transcription	Aorta	Aorta
9	chr2:172618800-172640800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:172619000-172638800	Weak transcription	Primary T cells from cord blood	blood
11	chr2:172619000-172641000	Weak transcription	Spleen	Spleen
12	chr2:172619200-172638600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:172619200-172640800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:172619200-172641000	Weak transcription	Thymus	Thymus
15	chr2:172619200-172641600	Weak transcription	Gastric	stomach
16	chr2:172619200-172641800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:172619600-172640200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:172620200-172641400	Weak transcription	NHEK	skin
19	chr2:172620400-172638600	Weak transcription	Primary B cells from cord blood	blood
20	chr2:172620400-172638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:172620400-172638600	Weak transcription	HSMM	muscle
22	chr2:172620400-172641000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:172620400-172641600	Weak transcription	HUVEC	blood vessel
24	chr2:172620400-172641800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:172620600-172640000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:172620800-172639600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:172620800-172640600	Weak transcription	Left Ventricle	heart
28	chr2:172620800-172640800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:172621000-172640000	Weak transcription	Osteobl	bone
30	chr2:172621000-172648000	Weak transcription	HSMMtube	muscle
31	chr2:172624600-172640200	Weak transcription	Right Ventricle	heart
32	chr2:172624600-172640200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:172628800-172640400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:172631400-172640000	Weak transcription	Brain Germinal Matrix	brain
35	chr2:172633400-172646200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:172633800-172641600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:172634200-172635400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:172634200-172635400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
39	chr2:172634400-172635400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:172634600-172635400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr2:172634600-172635400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:172634600-172635400	Strong transcription	Brain Angular Gyrus	brain
43	chr2:172634600-172635400	ZNF genes & repeats	Brain Hippocampus Middle	brain
44	chr2:172634600-172635600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:172634600-172635600	ZNF genes & repeats	Liver	Liver
46	chr2:172634600-172635600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
47	chr2:172634800-172635400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:172634800-172635400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
49	chr2:172634800-172635400	ZNF genes & repeats	NHDF-Ad	bronchial
50	chr2:172634800-172635600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood

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