Variant report

Variant	rs62248905
Chromosome Location	chr3:47274082-47274083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11130123	0.81[EUR][1000 genomes]
rs11130124	0.80[EUR][1000 genomes]
rs11130126	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714373	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11915074	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11920354	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11920853	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11921117	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11925560	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12493425	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12715421	0.86[AFR][1000 genomes]
rs13094438	0.89[EUR][1000 genomes]
rs1466740	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1466741	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1811652	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2088135	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276853	0.89[EUR][1000 genomes]
rs2276854	0.89[EUR][1000 genomes]
rs4018905	0.82[AFR][1000 genomes]
rs4683322	0.82[AFR][1000 genomes]
rs56250009	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57756484	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58956475	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62246451	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62246455	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6414435	0.84[AFR][1000 genomes]
rs6414436	0.82[AFR][1000 genomes]
rs6442055	0.86[AFR][1000 genomes]
rs6442059	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6766230	0.82[ASN][1000 genomes]
rs6767907	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs6768221	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6773521	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6777145	0.83[AFR][1000 genomes]
rs6781941	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791062	0.80[ASN][1000 genomes]
rs6791842	0.89[EUR][1000 genomes]
rs73069104	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7433300	0.84[AFR][1000 genomes]
rs7620997	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7632501	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311403	0.82[AFR][1000 genomes]
rs9812878	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9818382	0.82[ASN][1000 genomes]
rs9821119	0.83[ASN][1000 genomes]
rs9837343	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs9844122	0.86[AFR][1000 genomes]
rs9845728	0.88[AFR][1000 genomes]
rs9854790	0.88[AFR][1000 genomes]
rs9858443	0.86[AFR][1000 genomes]
rs9875235	0.83[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
rs62248905	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs62248905	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
3	chr3:47263000-47275600	Weak transcription	HSMMtube	muscle
4	chr3:47263600-47276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:47264200-47322200	Weak transcription	Gastric	stomach
6	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:47266800-47276400	Weak transcription	Fetal Intestine Small	intestine
8	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:47267200-47308000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:47267400-47281400	Weak transcription	Fetal Stomach	stomach
11	chr3:47267400-47284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:47267400-47287200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:47269800-47275000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:47269800-47276400	Weak transcription	Lung	lung
15	chr3:47269800-47281000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:47269800-47281200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:47269800-47288400	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:47270000-47277800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:47270000-47284600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:47270200-47276600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:47270200-47288600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:47270400-47275800	Weak transcription	Liver	Liver
23	chr3:47270600-47286800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:47270800-47307800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:47271200-47281000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:47271400-47308000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:47272600-47288200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:47273200-47276600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr3:47273600-47277000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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