Variant report

Variant	rs9828959
Chromosome Location	chr3:48091207-48091208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48086229..48089138-chr3:48089588..48092474,3	K562	blood:
2	chr3:48089386..48091329-chr3:48099273..48101274,2	K562	blood:
3	chr3:48086308..48089138-chr3:48089588..48092481,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1013431	0.88[EUR][1000 genomes]
rs11130152	0.86[EUR][1000 genomes]
rs11130154	0.89[EUR][1000 genomes]
rs11711129	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11924107	0.89[EUR][1000 genomes]
rs13074973	0.89[EUR][1000 genomes]
rs13075457	0.86[EUR][1000 genomes]
rs13075795	0.87[EUR][1000 genomes]
rs13081463	0.89[EUR][1000 genomes]
rs13085054	0.81[EUR][1000 genomes]
rs13089844	0.81[EUR][1000 genomes]
rs1530646	0.89[EUR][1000 genomes]
rs1550914	0.89[EUR][1000 genomes]
rs2034963	0.81[ASN][1000 genomes]
rs2053767	0.89[EUR][1000 genomes]
rs2121754	0.89[EUR][1000 genomes]
rs2166770	0.89[EUR][1000 genomes]
rs2166772	0.89[EUR][1000 genomes]
rs28637561	0.89[EUR][1000 genomes]
rs35314534	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35689209	0.85[EUR][1000 genomes]
rs4293721	0.89[EUR][1000 genomes]
rs4296617	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4392441	0.90[EUR][1000 genomes]
rs4599334	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858876	0.88[EUR][1000 genomes]
rs4858880	0.84[EUR][1000 genomes]
rs4858881	0.84[EUR][1000 genomes]
rs4858882	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858887	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5012971	0.90[EUR][1000 genomes]
rs56067795	0.87[EUR][1000 genomes]
rs62260830	0.80[EUR][1000 genomes]
rs6442090	0.89[EUR][1000 genomes]
rs6442091	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6442094	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6442096	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442099	0.83[EUR][1000 genomes]
rs6442101	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6768318	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6770467	0.89[EUR][1000 genomes]
rs6770477	0.89[EUR][1000 genomes]
rs6773208	0.87[EUR][1000 genomes]
rs6791834	0.86[EUR][1000 genomes]
rs6803741	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6804520	0.81[EUR][1000 genomes]
rs6806820	0.87[EUR][1000 genomes]
rs7374516	0.89[EUR][1000 genomes]
rs7426976	0.89[EUR][1000 genomes]
rs7427418	0.89[EUR][1000 genomes]
rs7430879	0.89[EUR][1000 genomes]
rs7430913	0.89[EUR][1000 genomes]
rs7431567	0.84[AMR][1000 genomes]
rs7618163	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7620736	0.86[EUR][1000 genomes]
rs7627645	0.90[EUR][1000 genomes]
rs7642590	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649981	0.89[EUR][1000 genomes]
rs9811277	0.89[EUR][1000 genomes]
rs9814961	0.89[EUR][1000 genomes]
rs9846062	0.88[EUR][1000 genomes]
rs9854454	0.89[EUR][1000 genomes]
rs9860485	0.86[EUR][1000 genomes]
rs9862913	0.89[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9828959	MRPS18AP1	cis	Nerve Tibial	GTEx
rs9828959	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs9828959	ZNF589	cis	Artery Tibial	GTEx
rs9828959	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs9828959	MRPS18AP1	cis	Artery Tibial	GTEx
rs9828959	MRPS18AP1	cis	Thyroid	GTEx
rs9828959	ZNF589	cis	Nerve Tibial	GTEx
rs9828959	NME6	cis	Esophagus Muscularis	GTEx
rs9828959	MRPS18AP1	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 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	chr3:48059800-48093600	Weak transcription	Gastric	stomach
4	chr3:48064400-48128800	Weak transcription	Esophagus	oesophagus
5	chr3:48074800-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:48075800-48102600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:48076200-48094200	Weak transcription	Aorta	Aorta
8	chr3:48076400-48100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:48081000-48093800	Weak transcription	Pancreas	Pancrea
10	chr3:48081200-48093600	Weak transcription	Psoas Muscle	Psoas
11	chr3:48081400-48098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:48081400-48110600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:48081600-48092000	Weak transcription	Stomach Mucosa	stomach
15	chr3:48081600-48092400	Weak transcription	Brain Germinal Matrix	brain
16	chr3:48081600-48093200	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:48081600-48096400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr3:48081600-48096400	Weak transcription	Fetal Brain Female	brain
19	chr3:48081600-48099200	Weak transcription	Ovary	ovary
20	chr3:48081600-48099600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:48081600-48099600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:48081600-48099800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:48081600-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:48081600-48100600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:48081600-48105800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:48081800-48092000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:48081800-48093400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:48081800-48094000	Weak transcription	Fetal Kidney	kidney
29	chr3:48081800-48096400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:48081800-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:48081800-48100400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:48082000-48096400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:48082000-48105600	Weak transcription	Small Intestine	intestine
35	chr3:48082200-48092000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:48082200-48096600	Weak transcription	Fetal Intestine Large	intestine
37	chr3:48082200-48105800	Weak transcription	Right Ventricle	heart
38	chr3:48082200-48115000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr3:48083600-48099600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:48083800-48092000	Weak transcription	Placenta	Placenta
41	chr3:48083800-48092200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:48083800-48093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:48083800-48093400	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:48083800-48093600	Weak transcription	Brain Substantia Nigra	brain
45	chr3:48083800-48094200	Weak transcription	Brain Angular Gyrus	brain
46	chr3:48083800-48100400	Weak transcription	Right Atrium	heart
47	chr3:48084000-48093600	Weak transcription	Left Ventricle	heart
48	chr3:48084000-48111800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:48084400-48093400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:48084400-48099400	Weak transcription	NH-A	brain

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