Variant report

Variant	rs4974112
Chromosome Location	chr3:51320800-51320801
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10510757	0.94[MEX][hapmap];0.87[TSI][hapmap]
rs12485331	0.84[EUR][1000 genomes]
rs12485754	0.84[EUR][1000 genomes]
rs12487468	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12487496	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12489219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490026	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12491836	0.89[EUR][1000 genomes]
rs12492615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs12492690	0.89[EUR][1000 genomes]
rs12493034	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493323	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493978	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs12495561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496830	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1480366	1.00[ASW][hapmap];0.94[LWK][hapmap];0.88[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs17051685	1.00[ASW][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes]
rs17051799	1.00[ASW][hapmap]
rs17051802	1.00[ASW][hapmap];0.94[LWK][hapmap];0.91[YRI][hapmap]
rs1809388	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1842394	0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2061949	0.94[MEX][hapmap]
rs2086395	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101056	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2127654	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170177	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306430	0.83[CHB][hapmap]
rs2306431	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs2355946	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762711	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828395	0.83[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs4130473	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs4346580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4468966	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs4927961	0.89[EUR][1000 genomes]
rs4974096	0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs4974100	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56052360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57406588	0.89[EUR][1000 genomes]
rs58201844	0.83[AMR][1000 genomes]
rs58911602	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59129045	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59682667	0.89[EUR][1000 genomes]
rs59834534	0.89[EUR][1000 genomes]
rs60128296	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60461297	0.89[EUR][1000 genomes]
rs60567238	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60740654	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61660900	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6792254	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72936442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72936462	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941919	0.89[EUR][1000 genomes]
rs72943166	0.89[EUR][1000 genomes]
rs72948197	0.89[EUR][1000 genomes]
rs72948200	0.89[EUR][1000 genomes]
rs72953143	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953162	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72953175	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751076	0.83[CHD][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes]
rs880477	0.91[YRI][hapmap]
rs880478	0.83[CHB][hapmap];0.84[AMR][1000 genomes]
rs9817077	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9817872	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9819195	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs9829057	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes]
rs9856134	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs9878592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880909	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats 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 target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4974112	MAPKAPK3	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51298000-51320800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:51299600-51320800	Weak transcription	Brain Germinal Matrix	brain
3	chr3:51308200-51323000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:51313000-51322800	Weak transcription	HSMMtube	muscle
5	chr3:51313000-51323800	Weak transcription	Fetal Brain Male	brain
6	chr3:51313400-51321800	Weak transcription	Right Ventricle	heart
7	chr3:51313400-51322800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:51315400-51350000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:51317800-51322200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:51318000-51322000	Weak transcription	Brain Anterior Caudate	brain
11	chr3:51318200-51320800	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:51318200-51328600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:51318600-51324400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:51319400-51322800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:51319600-51322400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:51319600-51324000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:51319600-51324200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:51319800-51321000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:51319800-51321600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:51319800-51323800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:51320000-51321200	Enhancers	Osteobl	bone
22	chr3:51320000-51321400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:51320000-51321400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:51320000-51322200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:51320000-51322600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:51320000-51324200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:51320400-51321200	Flanking Active TSS	NH-A	brain
28	chr3:51320400-51321600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:51320600-51321000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:51320600-51321000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:51320600-51321000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:51320600-51321000	Flanking Active TSS	HMEC	breast
33	chr3:51320600-51321000	Flanking Active TSS	NHEK	skin
34	chr3:51320600-51321200	Enhancers	HSMM	muscle
35	chr3:51320600-51321400	Enhancers	Primary T cells from cord blood	blood
36	chr3:51320600-51321800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:51320600-51321800	Strong transcription	Fetal Brain Female	brain
38	chr3:51320600-51322600	Strong transcription	Brain Angular Gyrus	brain
39	chr3:51320800-51321200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:51320800-51322000	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:51320800-51322800	Strong transcription	Brain Hippocampus Middle	brain
42	chr3:51320800-51323000	Strong transcription	Brain Germinal Matrix	brain

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