Variant report

Variant	rs10446426
Chromosome Location	chr3:48170521-48170522
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1013431	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11130152	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11130154	0.84[ASN][1000 genomes]
rs11130155	0.86[CEU][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11710866	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714518	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12486714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12493348	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13074973	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13075795	0.81[ASN][1000 genomes]
rs13080997	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13085054	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13089844	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1530646	0.84[ASN][1000 genomes]
rs1550914	0.82[ASN][1000 genomes]
rs2034963	0.99[EUR][1000 genomes]
rs2053767	0.82[ASN][1000 genomes]
rs2121754	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2166770	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs2166772	0.81[ASN][1000 genomes]
rs2361683	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2361684	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28637561	0.81[ASN][1000 genomes]
rs34597784	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35689209	0.83[EUR][1000 genomes]
rs4293721	0.81[ASN][1000 genomes]
rs4392441	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4599334	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4858810	0.96[CEU][hapmap]
rs4858876	0.83[ASN][1000 genomes]
rs4858880	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858881	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4858887	0.81[EUR][1000 genomes]
rs5012971	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442090	0.82[ASN][1000 genomes]
rs6442101	0.96[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs6442102	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6766641	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6770467	0.81[ASN][1000 genomes]
rs6770477	0.81[ASN][1000 genomes]
rs6773208	0.82[ASN][1000 genomes]
rs6777081	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791834	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793477	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6803741	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6804520	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6806820	0.82[ASN][1000 genomes]
rs7374482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374516	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs7426976	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs7427418	0.88[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs7427648	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430879	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7430913	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7620736	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7627645	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642590	0.96[CEU][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs7649981	0.82[ASN][1000 genomes]
rs936428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811277	0.82[ASN][1000 genomes]
rs9814961	0.81[ASN][1000 genomes]
rs9825114	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs9846062	0.82[ASN][1000 genomes]
rs9854454	0.82[ASN][1000 genomes]
rs9862913	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats 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 miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs10446426	ZNF589	cis	Whole Blood	GTEx
rs10446426	MRPS18AP1	cis	Thyroid	GTEx
rs10446426	MRPS18AP1	cis	lung	GTEx
rs10446426	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs10446426	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs10446426	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs10446426	ZNF589	cis	Adipose Subcutaneous	GTEx
rs10446426	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs10446426	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10446426	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs10446426	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs10446426	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs10446426	CDC25A	cis	Muscle Skeletal	GTEx
rs10446426	ZNF589	cis	Thyroid	GTEx
rs10446426	ZNF589	cis	Esophagus Mucosa	GTEx
rs10446426	MRPS18AP1	cis	Artery Tibial	GTEx
rs10446426	ZNF589	cis	Nerve Tibial	GTEx
rs10446426	NME6	cis	Esophagus Muscularis	GTEx
rs10446426	CDC25A	cis	Thyroid	GTEx
rs10446426	MRPS18AP1	cis	Nerve Tibial	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48161200-48171200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:48164400-48172000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48165200-48171600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:48167000-48171400	Weak transcription	Placenta	Placenta
5	chr3:48167000-48171400	Weak transcription	HepG2	liver
6	chr3:48167000-48171400	Weak transcription	HSMM	muscle
7	chr3:48167000-48177400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:48167200-48171200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:48167200-48171200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:48167200-48171200	Weak transcription	Ovary	ovary
11	chr3:48167200-48171200	Weak transcription	HSMMtube	muscle
12	chr3:48167200-48171200	Weak transcription	NHDF-Ad	bronchial
13	chr3:48167200-48171200	Weak transcription	Osteobl	bone
14	chr3:48167200-48178800	Weak transcription	NHEK	skin
15	chr3:48167400-48171200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:48167400-48171200	Weak transcription	NH-A	brain
17	chr3:48167400-48171200	Weak transcription	NHLF	lung
18	chr3:48167400-48171400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:48167600-48171200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:48167600-48171200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:48167600-48171200	Weak transcription	Adipose Nuclei	Adipose
22	chr3:48167600-48172400	Weak transcription	Hela-S3	cervix
23	chr3:48167800-48171400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:48167800-48171400	Weak transcription	Fetal Thymus	thymus
25	chr3:48167800-48171600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:48167800-48171800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:48167800-48181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:48169200-48171200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:48170000-48170600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:48170200-48170600	Enhancers	GM12878-XiMat	blood
31	chr3:48170200-48170800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:48170200-48170800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:48170400-48171800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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