Variant report

Variant	rs7642590
Chromosome Location	chr3:48099750-48099751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48098371..48102130-chr3:48128885..48131500,4	K562	blood:
2	chr3:48098552..48101007-chr3:48128885..48131500,2	K562	blood:
3	chr3:48089386..48091329-chr3:48099273..48101274,2	K562	blood:
4	chr3:48099186..48101154-chr3:48126536..48128244,2	K562	blood:

Variant related genes	Relation type
ENSG00000047849	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs1013431	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10446426	0.82[EUR][1000 genomes]
rs1060407	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs11130152	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs11130154	0.96[EUR][1000 genomes]
rs11130155	0.83[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1137524	0.86[EUR][1000 genomes]
rs11707679	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs11710866	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11711129	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11714518	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11720151	0.96[CEU][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11924107	0.85[EUR][1000 genomes]
rs12486714	0.96[CEU][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12493348	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13074973	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes]
rs13075457	0.93[EUR][1000 genomes]
rs13075795	0.95[EUR][1000 genomes]
rs13080997	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13081463	0.87[EUR][1000 genomes]
rs13085054	0.96[CEU][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap]
rs13089844	0.82[EUR][1000 genomes]
rs13093830	0.86[EUR][1000 genomes]
rs1530646	0.96[EUR][1000 genomes]
rs1550914	0.96[EUR][1000 genomes]
rs1684942	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs184388	0.86[EUR][1000 genomes]
rs2034963	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2053767	0.96[EUR][1000 genomes]
rs2121754	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes]
rs2166770	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2166772	0.96[EUR][1000 genomes]
rs2361683	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2361684	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631721	0.83[EUR][1000 genomes]
rs28637561	0.96[EUR][1000 genomes]
rs2882668	0.86[EUR][1000 genomes]
rs319681	0.82[EUR][1000 genomes]
rs319682	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs319684	0.86[EUR][1000 genomes]
rs319685	0.86[EUR][1000 genomes]
rs319686	0.86[EUR][1000 genomes]
rs319687	0.81[EUR][1000 genomes]
rs319688	0.81[EUR][1000 genomes]
rs319689	0.85[EUR][1000 genomes]
rs319690	0.84[EUR][1000 genomes]
rs319691	0.80[EUR][1000 genomes]
rs319692	0.83[EUR][1000 genomes]
rs319696	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs34025851	0.86[EUR][1000 genomes]
rs34597784	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34750113	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35199727	0.86[EUR][1000 genomes]
rs35314534	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35689209	0.97[EUR][1000 genomes]
rs3732529	0.86[EUR][1000 genomes]
rs4293721	0.96[EUR][1000 genomes]
rs4296617	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4392441	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4599334	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858810	0.96[CEU][hapmap]
rs4858871	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs4858876	0.93[EUR][1000 genomes]
rs4858880	0.96[EUR][1000 genomes]
rs4858881	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4858882	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858887	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5012971	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56067795	0.85[EUR][1000 genomes]
rs60446735	0.86[EUR][1000 genomes]
rs62260830	0.86[EUR][1000 genomes]
rs6442090	0.96[EUR][1000 genomes]
rs6442091	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442094	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442096	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442099	0.82[EUR][1000 genomes]
rs6442101	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442102	0.96[CEU][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6763824	0.84[CEU][hapmap]
rs6766641	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6766754	0.82[JPT][hapmap]
rs6768318	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6770467	0.96[EUR][1000 genomes]
rs6770477	0.96[EUR][1000 genomes]
rs6771889	0.88[ASW][hapmap]
rs6772396	0.86[EUR][1000 genomes]
rs6773208	0.94[EUR][1000 genomes]
rs6777081	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6783629	0.85[EUR][1000 genomes]
rs6791834	0.98[EUR][1000 genomes]
rs6797587	0.81[MEX][hapmap]
rs6803741	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6804520	0.82[EUR][1000 genomes]
rs6806820	0.95[EUR][1000 genomes]
rs7374376	0.82[JPT][hapmap]
rs7374482	0.96[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs7374516	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7426976	0.96[CEU][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7427418	0.92[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7427648	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7430879	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7430913	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs7431567	0.84[AMR][1000 genomes]
rs7618163	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7619882	0.87[EUR][1000 genomes]
rs7620736	0.98[EUR][1000 genomes]
rs7627645	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649981	0.96[EUR][1000 genomes]
rs7651237	0.83[EUR][1000 genomes]
rs7653368	0.86[EUR][1000 genomes]
rs777015	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs777017	0.86[EUR][1000 genomes]
rs796566	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs810334	0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs936428	0.96[CEU][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs9811277	0.96[EUR][1000 genomes]
rs9812875	0.87[EUR][1000 genomes]
rs9814961	0.96[EUR][1000 genomes]
rs9825114	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9828959	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9842649	0.86[EUR][1000 genomes]
rs9846062	0.95[EUR][1000 genomes]
rs9854454	0.96[EUR][1000 genomes]
rs9860485	0.93[EUR][1000 genomes]
rs9862913	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7642590	MRPS18AP1	cis	Thyroid	GTEx
rs7642590	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs7642590	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7642590	NME6	cis	Esophagus Muscularis	GTEx
rs7642590	ZNF589	cis	cerebellum	SCAN
rs7642590	ZNF589	cis	Artery Tibial	GTEx
rs7642590	ZNF589	cis	Whole Blood	GTEx
rs7642590	ZNF589	cis	Nerve Tibial	GTEx
rs7642590	HYAL2	cis	cerebellum	SCAN
rs7642590	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7642590	CDC25A	cis	cerebellum	SCAN
rs7642590	ZNF589	cis	parietal	SCAN
rs7642590	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7642590	SMARCC1	cis	cerebellum	SCAN
rs7642590	MRPS18AP1	cis	lung	GTEx
rs7642590	MRPS18AP1	cis	Artery Tibial	GTEx
rs7642590	CDC25A	cis	Thyroid	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	chr3:48059600-48128800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
4	chr3:48074800-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:48075800-48102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:48076400-48100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:48081400-48110600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:48081600-48099800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:48081600-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:48081600-48100600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:48081600-48105800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:48081800-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:48082000-48105600	Weak transcription	Small Intestine	intestine
16	chr3:48082200-48105800	Weak transcription	Right Ventricle	heart
17	chr3:48082200-48115000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:48083800-48100400	Weak transcription	Right Atrium	heart
19	chr3:48084000-48111800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:48084400-48099800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:48084400-48100000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:48086400-48100400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:48087600-48099800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:48089000-48099800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:48089200-48104600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:48089400-48128400	Weak transcription	Thymus	Thymus
27	chr3:48089400-48128600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:48089600-48128400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:48089800-48128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:48089800-48128800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:48090000-48105400	Weak transcription	NHEK	skin
32	chr3:48091000-48099800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:48091000-48105200	Weak transcription	HSMMtube	muscle
34	chr3:48091000-48106200	Weak transcription	HUVEC	blood vessel
35	chr3:48091000-48110200	Weak transcription	HepG2	liver
36	chr3:48091200-48099800	Weak transcription	Dnd41	blood
37	chr3:48091200-48100400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:48091200-48100600	Weak transcription	Lung	lung
39	chr3:48091200-48102400	Weak transcription	Fetal Thymus	thymus
40	chr3:48091200-48110000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:48091200-48110600	Weak transcription	Liver	Liver
42	chr3:48091200-48110800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:48091400-48111400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:48091400-48112400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:48092400-48099800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:48092400-48111000	Weak transcription	Fetal Stomach	stomach
47	chr3:48092600-48100400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:48092600-48110800	Weak transcription	Fetal Lung	lung
49	chr3:48092800-48102800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:48093800-48128400	Weak transcription	Spleen	Spleen

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