Variant report

Variant	rs6442091
Chromosome Location	chr3:48043058-48043059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48038125..48041271-chr3:48041821..48047334,6	K562	blood:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1013431	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1060407	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1061003	0.80[EUR][1000 genomes]
rs11130152	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130154	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130155	0.85[EUR][1000 genomes]
rs1137524	0.89[EUR][1000 genomes]
rs11707679	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710866	0.85[EUR][1000 genomes]
rs11711129	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11714518	0.82[EUR][1000 genomes]
rs11720151	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11924107	0.83[EUR][1000 genomes]
rs12486714	0.83[EUR][1000 genomes]
rs12493348	0.85[EUR][1000 genomes]
rs13074973	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13075457	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13075795	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13080997	0.83[EUR][1000 genomes]
rs13081463	0.85[EUR][1000 genomes]
rs13081701	0.80[EUR][1000 genomes]
rs13093830	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1530646	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1550914	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1665982	0.84[AFR][1000 genomes]
rs1684942	0.82[EUR][1000 genomes]
rs184388	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2053767	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2121754	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2166770	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2166772	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2361683	0.83[EUR][1000 genomes]
rs2361684	0.83[EUR][1000 genomes]
rs2631721	0.86[EUR][1000 genomes]
rs28637561	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2882668	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs319681	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs319682	0.85[EUR][1000 genomes]
rs319684	0.89[EUR][1000 genomes]
rs319685	0.89[EUR][1000 genomes]
rs319686	0.89[EUR][1000 genomes]
rs319687	0.83[EUR][1000 genomes]
rs319688	0.84[EUR][1000 genomes]
rs319689	0.87[EUR][1000 genomes]
rs319690	0.87[EUR][1000 genomes]
rs319691	0.83[EUR][1000 genomes]
rs319692	0.86[EUR][1000 genomes]
rs319693	0.81[ASN][1000 genomes]
rs319695	0.81[ASN][1000 genomes]
rs319696	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34025851	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34597784	0.83[EUR][1000 genomes]
rs34750113	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35199727	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35314534	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35689209	0.94[EUR][1000 genomes]
rs35943823	0.80[AFR][1000 genomes]
rs3732529	0.89[EUR][1000 genomes]
rs4293721	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4296617	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392441	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4599334	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858871	0.88[EUR][1000 genomes]
rs4858876	0.95[EUR][1000 genomes]
rs4858880	0.93[EUR][1000 genomes]
rs4858881	0.92[EUR][1000 genomes]
rs4858882	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858887	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5012971	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56067795	0.83[EUR][1000 genomes]
rs60446735	0.89[EUR][1000 genomes]
rs62260830	0.82[EUR][1000 genomes]
rs6442090	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442094	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6442096	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6442101	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442102	0.83[EUR][1000 genomes]
rs6766641	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768318	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6770467	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6770477	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6772396	0.89[EUR][1000 genomes]
rs6773208	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6777081	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783629	0.86[EUR][1000 genomes]
rs6791834	0.95[EUR][1000 genomes]
rs6803741	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6806820	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7374482	0.82[EUR][1000 genomes]
rs7374516	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7426976	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7427418	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7427648	0.82[EUR][1000 genomes]
rs7430879	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7430913	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431567	0.91[AMR][1000 genomes]
rs7618163	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7619882	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7620736	0.95[EUR][1000 genomes]
rs7627645	0.99[EUR][1000 genomes]
rs7642590	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7649981	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651237	0.80[EUR][1000 genomes]
rs7653368	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs777014	0.82[EUR][1000 genomes]
rs777015	0.89[EUR][1000 genomes]
rs777017	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs796566	0.89[EUR][1000 genomes]
rs800762	0.82[EUR][1000 genomes]
rs810334	0.89[EUR][1000 genomes]
rs936428	0.82[EUR][1000 genomes]
rs9811277	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9812875	0.90[EUR][1000 genomes]
rs9814961	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9825114	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9828959	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9842649	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9846062	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9850154	0.83[AFR][1000 genomes]
rs9854454	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860485	0.98[EUR][1000 genomes]
rs9862913	1.00[EUR][1000 genomes];0.87[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	esv3335628	chr3:48010796-48074001	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6442091	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6442091	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6442091	MRPS18AP1	cis	Artery Tibial	GTEx
rs6442091	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs6442091	NME6	cis	Esophagus Muscularis	GTEx
rs6442091	MRPS18AP1	cis	lung	GTEx
rs6442091	ZNF589	cis	Artery Tibial	GTEx
rs6442091	CDC25A	cis	Thyroid	GTEx
rs6442091	ZNF589	cis	Nerve Tibial	GTEx
rs6442091	MRPS18AP1	cis	Thyroid	GTEx
rs6442091	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6442091	ZNF589	cis	Whole Blood	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48003800-48047200	Weak transcription	Lung	lung
2	chr3:48003800-48060600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:48004000-48043600	Weak transcription	Small Intestine	intestine
4	chr3:48004000-48045400	Weak transcription	Placenta	Placenta
5	chr3:48004000-48046200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:48004000-48050600	Weak transcription	Pancreas	Pancrea
7	chr3:48013400-48053400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:48016600-48055800	Weak transcription	Esophagus	oesophagus
9	chr3:48018000-48057200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr3:48019400-48043400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:48019400-48054800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:48027200-48063600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:48029200-48055200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:48029200-48057400	Weak transcription	Spleen	Spleen
15	chr3:48030400-48043200	Weak transcription	Thymus	Thymus
16	chr3:48031600-48054600	Weak transcription	HUVEC	blood vessel
17	chr3:48032000-48053600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:48033200-48049800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:48035400-48057400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:48036000-48049800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:48036000-48052600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:48036000-48057200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:48037800-48048600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:48038000-48049600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:48038000-48049600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:48038000-48049600	Weak transcription	Fetal Intestine Small	intestine
27	chr3:48038000-48049600	Weak transcription	Fetal Stomach	stomach
28	chr3:48038000-48049800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:48038000-48050000	Weak transcription	Gastric	stomach
30	chr3:48038000-48050200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:48038000-48051000	Weak transcription	Right Atrium	heart
32	chr3:48038000-48053000	Weak transcription	HSMMtube	muscle
33	chr3:48038000-48054800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:48038200-48045000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:48038200-48047600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr3:48038200-48047800	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:48038200-48048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:48038200-48052800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:48038200-48053200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:48038200-48053200	Weak transcription	Fetal Kidney	kidney
41	chr3:48038200-48053400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:48038200-48054200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:48038200-48054800	Weak transcription	A549	lung
44	chr3:48038200-48055200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:48038400-48047800	Weak transcription	Right Ventricle	heart
46	chr3:48038400-48054200	Weak transcription	Fetal Lung	lung
47	chr3:48038600-48050400	Weak transcription	Adipose Nuclei	Adipose
48	chr3:48038600-48053800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:48038600-48055200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:48039200-48049800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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