Variant report

Variant	rs6442094
Chromosome Location	chr3:48079577-48079578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1013431	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1060407	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130152	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130154	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130155	0.81[EUR][1000 genomes]
rs1137524	0.82[EUR][1000 genomes]
rs11707679	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11710866	0.81[EUR][1000 genomes]
rs11711129	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11720151	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11924107	0.84[EUR][1000 genomes]
rs12493348	0.81[EUR][1000 genomes]
rs13074973	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13075457	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13075795	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13081463	0.85[EUR][1000 genomes]
rs13093830	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530646	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1550914	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs184388	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2053767	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2121754	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2166770	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2166772	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28637561	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2882668	0.82[EUR][1000 genomes]
rs319681	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319684	0.82[EUR][1000 genomes]
rs319685	0.82[EUR][1000 genomes]
rs319686	0.82[EUR][1000 genomes]
rs319689	0.81[EUR][1000 genomes]
rs319690	0.80[EUR][1000 genomes]
rs319696	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34025851	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34750113	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35199727	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35314534	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35689209	0.89[EUR][1000 genomes]
rs3732529	0.82[EUR][1000 genomes]
rs4293721	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4296617	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4392441	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4599334	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4858871	0.82[EUR][1000 genomes]
rs4858876	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858880	0.88[EUR][1000 genomes]
rs4858881	0.88[EUR][1000 genomes]
rs4858882	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858887	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5012971	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56067795	0.81[EUR][1000 genomes]
rs60446735	0.82[EUR][1000 genomes]
rs62260830	0.82[EUR][1000 genomes]
rs6442090	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442091	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442096	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442101	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6766641	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6768318	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6770467	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6770477	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6772396	0.82[EUR][1000 genomes]
rs6773208	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6777081	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6791834	0.91[EUR][1000 genomes]
rs6803741	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6806820	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7374516	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7426976	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7427418	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430879	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430913	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7431567	0.89[AMR][1000 genomes]
rs7618163	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7619882	0.83[EUR][1000 genomes]
rs7620736	0.91[EUR][1000 genomes]
rs7627645	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7642590	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649981	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7653368	0.82[EUR][1000 genomes]
rs777015	0.82[EUR][1000 genomes]
rs777017	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs796566	0.82[EUR][1000 genomes]
rs810334	0.82[EUR][1000 genomes]
rs9811277	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9812875	0.83[EUR][1000 genomes]
rs9814961	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9825114	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828959	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9842649	0.82[EUR][1000 genomes]
rs9846062	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9854454	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9860485	0.91[EUR][1000 genomes]
rs9862913	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6442094	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6442094	MRPS18AP1	cis	Thyroid	GTEx
rs6442094	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs6442094	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6442094	MRPS18AP1	cis	Artery Tibial	GTEx
rs6442094	ZNF589	cis	Nerve Tibial	GTEx
rs6442094	ZNF589	cis	Whole Blood	GTEx
rs6442094	NME6	cis	Esophagus Muscularis	GTEx
rs6442094	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48051200-48128000	Weak transcription	Primary B cells from cord blood	blood
2	chr3:48058400-48082400	Weak transcription	Spleen	Spleen
3	chr3:48058800-48080600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:48059200-48080600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
6	chr3:48059800-48090800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:48059800-48093600	Weak transcription	Gastric	stomach
8	chr3:48060800-48088800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:48060800-48089400	Weak transcription	Dnd41	blood
10	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
11	chr3:48065200-48080600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:48069000-48080800	Weak transcription	Fetal Kidney	kidney
13	chr3:48071400-48080400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:48071800-48081600	Enhancers	Fetal Heart	heart
15	chr3:48073400-48081800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:48074800-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:48075800-48080400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:48075800-48080400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:48075800-48080400	Weak transcription	Ovary	ovary
20	chr3:48075800-48080800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:48075800-48080800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:48075800-48102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48076000-48080000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:48076000-48080600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:48076000-48080600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:48076200-48079800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:48076200-48080000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:48076200-48080200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:48076200-48080200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:48076200-48080200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:48076200-48080200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:48076200-48080200	Weak transcription	HSMM	muscle
33	chr3:48076200-48080200	Weak transcription	K562	blood
34	chr3:48076200-48080400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr3:48076200-48080400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:48076200-48080400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:48076200-48080400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:48076200-48080400	Weak transcription	Stomach Mucosa	stomach
39	chr3:48076200-48080800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:48076200-48081000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:48076200-48094200	Weak transcription	Aorta	Aorta
42	chr3:48076400-48080000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:48076400-48080000	Weak transcription	Psoas Muscle	Psoas
44	chr3:48076400-48080200	Weak transcription	Osteobl	bone
45	chr3:48076400-48080400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr3:48076400-48080800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:48076400-48100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:48076600-48079600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:48076600-48079600	Weak transcription	Hela-S3	cervix
50	chr3:48076600-48080000	Weak transcription	HUVEC	blood vessel

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