Variant report

Variant	rs2088135
Chromosome Location	chr3:47280018-47280019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47279696..47282501-chr3:47283361..47286390,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47279894-47280059	ENSG00000227398
2	lnc-KLHL18-1	chr3:47279894-47280059	NONHSAT089478
3	lnc-KLHL18-1	chr3:47279894-47280059	NONHSAT089479
4	lnc-KLHL18-1	chr3:47279894-47280059	ENSG00000227398.3

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11130123	0.83[EUR][1000 genomes]
rs11130124	0.82[EUR][1000 genomes]
rs11130126	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710013	0.81[EUR][1000 genomes]
rs11714373	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719738	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11915074	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11920354	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11920853	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11921117	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11925560	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493425	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12715421	0.82[AFR][1000 genomes]
rs13094438	0.90[EUR][1000 genomes]
rs1466740	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466741	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1811652	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2132173	0.80[EUR][1000 genomes]
rs2276853	0.91[EUR][1000 genomes]
rs2276854	0.90[EUR][1000 genomes]
rs4683324	0.81[EUR][1000 genomes]
rs4683326	0.81[EUR][1000 genomes]
rs56250009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57756484	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58956475	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62246451	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62246455	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248905	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414435	0.83[AFR][1000 genomes]
rs6442055	0.82[AFR][1000 genomes]
rs6442059	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6766230	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6767907	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6768221	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6773521	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777145	0.80[AFR][1000 genomes]
rs6781941	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791062	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6791842	0.91[EUR][1000 genomes]
rs73069104	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7433300	0.83[AFR][1000 genomes]
rs7620997	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7632501	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7636423	0.80[EUR][1000 genomes]
rs9812878	0.80[ASN][1000 genomes]
rs9818382	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821119	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9837343	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.82[AFR][1000 genomes]
rs9845728	0.84[AFR][1000 genomes]
rs9854790	0.84[AFR][1000 genomes]
rs9858443	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1014457	chr3:47222292-47335175	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv536560	chr3:47222292-47335175	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	esv1799921	chr3:47259253-47283105	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2088135	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs2088135	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
2	chr3:47264200-47322200	Weak transcription	Gastric	stomach
3	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:47267400-47281400	Weak transcription	Fetal Stomach	stomach
7	chr3:47267400-47284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:47269800-47281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:47269800-47281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:47270000-47284600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:47270600-47286800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:47271200-47281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:47276200-47283000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:47276400-47305200	Weak transcription	Brain Anterior Caudate	brain
21	chr3:47276600-47283800	Weak transcription	Right Ventricle	heart
22	chr3:47276800-47281400	Weak transcription	Fetal Intestine Small	intestine
23	chr3:47276800-47284000	Weak transcription	HSMMtube	muscle
24	chr3:47276800-47284600	Weak transcription	Pancreas	Pancrea
25	chr3:47276800-47285200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:47276800-47285200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:47277000-47281400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:47277000-47288200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:47277000-47292000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:47277200-47281800	Weak transcription	HepG2	liver
31	chr3:47277400-47284600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:47277400-47285200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:47277600-47281600	Weak transcription	Lung	lung
34	chr3:47277600-47300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:47278000-47281400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:47278400-47281200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:47278400-47285800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:47279200-47286200	Weak transcription	Ovary	ovary
39	chr3:47279600-47281400	Weak transcription	Aorta	Aorta
40	chr3:47279800-47288800	Weak transcription	Brain Substantia Nigra	brain

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