Variant report

Variant	rs12335553
Chromosome Location	chr9:95297871-95297872
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10115290	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10116241	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10117680	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10118107	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10120329	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10121495	0.81[AMR][1000 genomes]
rs10123738	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125450	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10283572	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10429459	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10453241	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10514815	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1053441	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1053446	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1075397	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10761153	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10761154	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761158	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10761161	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10761164	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820969	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10820971	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10820986	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820988	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10820989	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10820990	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992322	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10992340	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992347	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10992365	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992375	0.81[ASN][1000 genomes]
rs11789163	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11795122	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12338938	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12343820	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12348488	0.81[AMR][1000 genomes]
rs13296623	0.82[AMR][1000 genomes]
rs13301492	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13301652	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1535754	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1924243	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1924244	0.81[AMR][1000 genomes]
rs2007837	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2025388	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2026585	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2094281	0.84[AFR][1000 genomes]
rs2104533	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274966	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2296666	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2296667	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2516567	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2761679	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2895219	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3739606	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3780347	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3927488	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4302908	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743874	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744133	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4744134	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4744135	0.80[AMR][1000 genomes]
rs4744136	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4744137	0.85[AFR][1000 genomes]
rs4744138	0.85[AFR][1000 genomes]
rs4744139	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6479419	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6479420	0.82[AMR][1000 genomes]
rs6479423	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7020874	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7023004	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7026361	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7031567	0.80[AMR][1000 genomes]
rs7045409	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7047089	0.82[AMR][1000 genomes]
rs747628	0.82[AFR][1000 genomes]
rs747629	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847534	0.85[AFR][1000 genomes]
rs7847929	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7849788	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7849927	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7850432	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7852510	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7853859	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7856204	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7863049	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7863234	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7864630	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7868640	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869742	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7872610	0.81[AFR][1000 genomes]
rs7872644	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7873390	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8067	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs927865	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9299404	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9299405	0.85[AFR][1000 genomes]
rs968040	0.85[AFR][1000 genomes]
rs987553	0.85[AFR][1000 genomes]
rs987554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1047337	chr9:95105638-95347484	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1052846	chr9:95291909-95366109	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12335553	NOL8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95269800-95298800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:95294800-95301200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:95296000-95301800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:95296400-95299600	Enhancers	HepG2	liver
5	chr9:95296600-95298800	Active TSS	Stomach Smooth Muscle	stomach
6	chr9:95296600-95299000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr9:95296800-95298000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr9:95296800-95298800	Active TSS	Rectal Smooth Muscle	rectum
9	chr9:95297000-95299200	Active TSS	Right Atrium	heart
10	chr9:95297200-95298200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:95297200-95301000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:95297400-95298000	Enhancers	Fetal Intestine Large	intestine
13	chr9:95297400-95298200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:95297400-95298200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:95297400-95298200	Weak transcription	Aorta	Aorta
16	chr9:95297400-95298200	Weak transcription	Brain Anterior Caudate	brain
17	chr9:95297400-95298200	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:95297400-95298200	Weak transcription	Fetal Intestine Small	intestine
19	chr9:95297400-95298400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:95297400-95298400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:95297400-95298400	Active TSS	Fetal Kidney	kidney
22	chr9:95297400-95298400	Weak transcription	Fetal Stomach	stomach
23	chr9:95297400-95298400	Weak transcription	Psoas Muscle	Psoas
24	chr9:95297400-95298400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:95297400-95298400	Weak transcription	Stomach Mucosa	stomach
26	chr9:95297400-95298400	Enhancers	GM12878-XiMat	blood
27	chr9:95297400-95298400	Weak transcription	HSMMtube	muscle
28	chr9:95297400-95298600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:95297400-95298800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr9:95297400-95298800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:95297400-95298800	Active TSS	Fetal Muscle Leg	muscle
32	chr9:95297400-95298800	Active TSS	NHLF	lung
33	chr9:95297400-95299000	Active TSS	Adipose Nuclei	Adipose
34	chr9:95297400-95299200	Active TSS	Fetal Lung	lung
35	chr9:95297400-95299200	Active TSS	Ovary	ovary
36	chr9:95297400-95299400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr9:95297400-95300000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:95297400-95300000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr9:95297400-95304600	Weak transcription	Left Ventricle	heart
40	chr9:95297600-95298000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:95297600-95298000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:95297600-95298000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr9:95297600-95298000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:95297600-95298000	Enhancers	Osteobl	bone
45	chr9:95297600-95298200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr9:95297600-95299200	Active TSS	NHDF-Ad	bronchial
47	chr9:95297800-95298000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:95297800-95298000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:95297800-95298600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:95297800-95299200	Active TSS	Liver	Liver

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