Variant report

Variant	rs2489166
Chromosome Location	chr10:38245597-38245598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10508861	0.82[AMR][1000 genomes]
rs1208578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208619	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1208621	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12243792	0.80[EUR][1000 genomes]
rs12412402	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12413083	0.93[ASN][1000 genomes]
rs12414618	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1735625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17608725	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176831	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176832	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1779073	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs200907	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200909	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200913	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs200914	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs200941	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2021651	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2178958	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293962	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2472153	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2472159	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2472160	0.84[ASN][1000 genomes]
rs2474542	0.86[ASN][1000 genomes]
rs2474545	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2474553	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480521	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2504137	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2505218	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2738221	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2753883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55742761	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59486180	0.81[EUR][1000 genomes]
rs766362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895468	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9418311	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1045684	chr10:37765361-38426204	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv540564	chr10:37765361-38426204	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1040704	chr10:37940024-38451917	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv1051121	chr10:38155991-38426204	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv540565	chr10:38155991-38426204	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv1052703	chr10:38174640-38266472	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv534122	chr10:38240258-38356008	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2489166	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2489166	ZNF37A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38236800-38249000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:38237800-38247200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr10:38238000-38248600	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:38238400-38253000	Weak transcription	Fetal Intestine Small	intestine
5	chr10:38238600-38246400	Strong transcription	Psoas Muscle	Psoas
6	chr10:38238800-38248600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr10:38239000-38247000	Strong transcription	Left Ventricle	heart
8	chr10:38239000-38249400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr10:38239200-38246600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr10:38239200-38248000	Strong transcription	Adipose Nuclei	Adipose
11	chr10:38239400-38247400	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr10:38239400-38247800	Strong transcription	Brain Hippocampus Middle	brain
13	chr10:38239400-38248200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr10:38239600-38245800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr10:38239600-38246400	Strong transcription	Brain Substantia Nigra	brain
16	chr10:38239600-38264400	Weak transcription	Fetal Heart	heart
17	chr10:38239600-38264600	Weak transcription	Stomach Mucosa	stomach
18	chr10:38240000-38246600	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr10:38240000-38247600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr10:38240200-38247800	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:38240400-38246800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr10:38240400-38247600	Strong transcription	Fetal Lung	lung
23	chr10:38240400-38249200	Strong transcription	Ovary	ovary
24	chr10:38240600-38247400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr10:38240600-38247400	Strong transcription	NHDF-Ad	bronchial
26	chr10:38240600-38247800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr10:38240600-38248200	Strong transcription	Fetal Muscle Leg	muscle
28	chr10:38240800-38246400	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr10:38240800-38264000	Weak transcription	NHLF	lung
30	chr10:38241000-38246000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr10:38241000-38246400	Strong transcription	Brain Germinal Matrix	brain
32	chr10:38241000-38246600	Strong transcription	Colon Smooth Muscle	Colon
33	chr10:38241000-38247400	Strong transcription	Brain Angular Gyrus	brain
34	chr10:38241000-38247400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr10:38241000-38247800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:38241000-38248200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr10:38241200-38247400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr10:38241200-38247400	Strong transcription	Brain Anterior Caudate	brain
39	chr10:38241200-38249600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr10:38241800-38249000	Weak transcription	Small Intestine	intestine
41	chr10:38241800-38264400	Weak transcription	NHEK	skin
42	chr10:38242000-38248400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr10:38242200-38246600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr10:38242200-38253600	Weak transcription	Esophagus	oesophagus
45	chr10:38242200-38253800	Weak transcription	Pancreas	Pancrea
46	chr10:38242400-38245800	Strong transcription	Osteobl	bone
47	chr10:38242400-38246200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr10:38242400-38246200	Weak transcription	Fetal Thymus	thymus
49	chr10:38242400-38247200	Strong transcription	Fetal Kidney	kidney
50	chr10:38242400-38247800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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