Variant report

Variant	rs11924107
Chromosome Location	chr3:48113624-48113625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1013431	0.82[EUR][1000 genomes]
rs11130154	0.83[EUR][1000 genomes]
rs11130155	0.86[AMR][1000 genomes]
rs11710866	0.83[AMR][1000 genomes]
rs11711129	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714518	0.81[AMR][1000 genomes]
rs12493348	0.81[AMR][1000 genomes]
rs13074973	0.83[EUR][1000 genomes]
rs13075457	0.81[EUR][1000 genomes]
rs13075795	0.81[EUR][1000 genomes]
rs13081463	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085054	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13089844	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530646	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1550914	0.83[EUR][1000 genomes]
rs2053767	0.83[EUR][1000 genomes]
rs2121754	0.83[EUR][1000 genomes]
rs2166770	0.83[EUR][1000 genomes]
rs2166772	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28637561	0.83[EUR][1000 genomes]
rs35314534	0.83[EUR][1000 genomes]
rs35689209	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4293721	0.83[EUR][1000 genomes]
rs4296617	0.83[EUR][1000 genomes]
rs4392441	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4599334	0.83[EUR][1000 genomes]
rs4858876	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4858880	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4858881	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858882	0.93[EUR][1000 genomes]
rs4858887	0.84[EUR][1000 genomes]
rs5012971	0.84[EUR][1000 genomes]
rs56067795	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6442090	0.83[EUR][1000 genomes]
rs6442091	0.83[EUR][1000 genomes]
rs6442094	0.84[EUR][1000 genomes]
rs6442096	0.85[EUR][1000 genomes]
rs6442099	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442101	0.85[EUR][1000 genomes]
rs6442102	0.80[AMR][1000 genomes]
rs6768318	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6770467	0.83[EUR][1000 genomes]
rs6770477	0.83[EUR][1000 genomes]
rs6773208	0.81[EUR][1000 genomes]
rs6791834	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6793477	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6803741	0.86[EUR][1000 genomes]
rs6804520	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6806820	0.82[EUR][1000 genomes]
rs7374516	0.83[EUR][1000 genomes]
rs7426976	0.83[EUR][1000 genomes]
rs7427418	0.83[EUR][1000 genomes]
rs7430879	0.83[EUR][1000 genomes]
rs7430913	0.83[EUR][1000 genomes]
rs7618163	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7620736	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7627645	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7642590	0.85[EUR][1000 genomes]
rs7649981	0.83[EUR][1000 genomes]
rs9811277	0.83[EUR][1000 genomes]
rs9814961	0.83[EUR][1000 genomes]
rs9828959	0.89[EUR][1000 genomes]
rs9846062	0.82[EUR][1000 genomes]
rs9854454	0.83[EUR][1000 genomes]
rs9860485	0.82[EUR][1000 genomes]
rs9862913	0.83[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11924107	MRPS18AP1	cis	Nerve Tibial	GTEx
rs11924107	CDC25A	cis	Muscle Skeletal	GTEx
rs11924107	MRPS18AP1	cis	Thyroid	GTEx
rs11924107	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs11924107	CDC25A	cis	Thyroid	GTEx
rs11924107	MRPS18AP1	cis	lung	GTEx
rs11924107	MRPS18AP1	cis	Artery Tibial	GTEx
rs11924107	ZNF589	cis	Nerve Tibial	GTEx
rs11924107	ZNF589	cis	Artery Tibial	GTEx
rs11924107	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs11924107	DHX30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 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	chr3:48081400-48128400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr3:48081800-48128400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:48082200-48115000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:48089400-48128400	Weak transcription	Thymus	Thymus
8	chr3:48089400-48128600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:48089600-48128400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:48089800-48128200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:48089800-48128800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:48093800-48128400	Weak transcription	Spleen	Spleen
13	chr3:48095000-48128400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:48096600-48126000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:48100800-48123200	Weak transcription	GM12878-XiMat	blood
16	chr3:48100800-48128400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:48100800-48128600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:48100800-48128800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:48101000-48116400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr3:48101600-48128200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr3:48103600-48128200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:48105000-48128200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:48105200-48125600	Weak transcription	Dnd41	blood
24	chr3:48105200-48128400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:48105600-48128200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:48106000-48126000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:48106000-48128400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:48106200-48118400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:48106600-48113800	Weak transcription	Aorta	Aorta
30	chr3:48106600-48113800	Weak transcription	Lung	lung
31	chr3:48106600-48116400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:48106600-48118200	Weak transcription	HMEC	breast
33	chr3:48106600-48128400	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:48106600-48128800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:48107000-48119200	Weak transcription	HUVEC	blood vessel
36	chr3:48107400-48125800	Weak transcription	Pancreas	Pancrea
37	chr3:48108400-48128800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:48108800-48128200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:48109000-48127600	Weak transcription	Brain Germinal Matrix	brain
40	chr3:48109000-48128400	Weak transcription	Fetal Brain Male	brain
41	chr3:48109600-48115200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:48110200-48128200	Weak transcription	Fetal Brain Female	brain
43	chr3:48110200-48128400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:48110800-48124000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:48111000-48113800	Strong transcription	Fetal Stomach	stomach
46	chr3:48111000-48119200	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:48111000-48123800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:48111000-48128400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:48111200-48118000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:48111200-48118200	Weak transcription	Osteobl	bone

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