Variant report

Variant	rs12487468
Chromosome Location	chr3:51389570-51389571
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10510757	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10510758	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12485610	0.89[ASN][1000 genomes]
rs12487426	0.89[ASN][1000 genomes]
rs12489219	0.83[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs12489414	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12490471	0.89[ASN][1000 genomes]
rs12490889	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12491048	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12492615	0.89[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs12492624	0.89[ASN][1000 genomes]
rs12493034	0.87[AMR][1000 genomes]
rs12493265	0.87[ASN][1000 genomes]
rs12493323	0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12493618	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12493857	0.89[ASN][1000 genomes]
rs12493978	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494462	0.89[ASN][1000 genomes]
rs12494979	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12495561	0.82[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13089799	0.84[ASN][1000 genomes]
rs13090348	0.93[ASN][1000 genomes]
rs1370124	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1480366	0.94[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs17051685	1.00[YRI][hapmap]
rs17051783	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051802	0.94[LWK][hapmap];1.00[YRI][hapmap]
rs17051811	0.84[ASN][1000 genomes]
rs17661242	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17712228	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1809388	0.87[AMR][1000 genomes]
rs1842394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2033703	0.92[ASN][1000 genomes]
rs2061949	0.88[MEX][hapmap]
rs2082992	0.88[ASN][1000 genomes]
rs2082993	0.86[ASN][1000 genomes]
rs2086395	0.87[AMR][1000 genomes]
rs2101056	0.89[CHB][hapmap]
rs2127654	0.83[AMR][1000 genomes]
rs2170177	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2217938	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241785	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304512	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306430	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2355946	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2356261	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356298	0.89[ASN][1000 genomes]
rs35536327	0.84[ASN][1000 genomes]
rs3749317	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3762711	0.87[AMR][1000 genomes]
rs3792408	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804766	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828395	0.89[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4130473	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs4346580	0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs4468966	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687553	0.86[ASN][1000 genomes]
rs4687563	0.86[ASN][1000 genomes]
rs4687601	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687605	0.89[ASN][1000 genomes]
rs4687610	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687656	0.88[ASN][1000 genomes]
rs4687691	0.86[ASN][1000 genomes]
rs4687731	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687777	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687794	0.86[ASN][1000 genomes]
rs4687803	0.84[AMR][1000 genomes]
rs4687811	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4687812	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687813	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974096	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4974098	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4974112	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]
rs55667499	0.86[ASN][1000 genomes]
rs55671465	0.81[ASN][1000 genomes]
rs56052360	0.87[AMR][1000 genomes]
rs56239081	0.89[ASN][1000 genomes]
rs56729479	0.89[ASN][1000 genomes]
rs57027950	0.93[ASN][1000 genomes]
rs57047724	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57603251	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57700326	0.82[ASN][1000 genomes]
rs57831708	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58059174	0.89[ASN][1000 genomes]
rs58201844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58568178	0.92[ASN][1000 genomes]
rs58807639	0.86[AFR][1000 genomes]
rs58836277	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58911602	0.87[AMR][1000 genomes]
rs59129045	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59563413	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59838596	0.87[ASN][1000 genomes]
rs59953568	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60128296	0.83[AMR][1000 genomes]
rs60567238	0.87[AMR][1000 genomes]
rs60606339	0.89[ASN][1000 genomes]
rs60740654	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs61233013	0.86[ASN][1000 genomes]
rs61419317	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61660900	0.87[AMR][1000 genomes]
rs61689323	0.87[ASN][1000 genomes]
rs72936442	0.86[AMR][1000 genomes]
rs72936462	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72945708	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72945713	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72951443	0.87[ASN][1000 genomes]
rs72953175	0.87[AMR][1000 genomes]
rs73834252	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834253	0.90[ASN][1000 genomes]
rs73834254	0.90[ASN][1000 genomes]
rs73834258	0.89[ASN][1000 genomes]
rs73837439	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73837442	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73837443	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs751076	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs753452	0.84[AFR][1000 genomes]
rs7642698	0.87[ASN][1000 genomes]
rs880477	1.00[YRI][hapmap]
rs880478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9817872	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9819195	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820140	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9827186	0.84[ASN][1000 genomes]
rs9829057	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9842600	0.86[ASN][1000 genomes]
rs9843583	0.85[ASN][1000 genomes]
rs9856134	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861019	0.81[ASN][1000 genomes]
rs9878592	0.83[CHB][hapmap];0.83[CHD][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv20206	chr3:51344873-51415825	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12487468	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs12487468	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51376800-51391800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:51376800-51392400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:51378000-51399800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:51378400-51389800	Weak transcription	Brain Substantia Nigra	brain
5	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
7	chr3:51379000-51390200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:51379000-51393800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:51379000-51414600	Weak transcription	Left Ventricle	heart
10	chr3:51379200-51393600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:51379200-51393800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:51379200-51399800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:51379400-51403400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:51380000-51398400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:51380000-51398400	Weak transcription	Aorta	Aorta
16	chr3:51381400-51392000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:51381800-51392200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:51382400-51389800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:51382800-51392200	Weak transcription	HSMMtube	muscle
20	chr3:51383000-51391000	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:51384200-51392400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:51384200-51393800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
24	chr3:51385400-51405600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:51386400-51405400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:51386600-51392200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:51387200-51392400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr3:51388000-51392400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:51388000-51393600	Weak transcription	Fetal Stomach	stomach
30	chr3:51388400-51400800	Strong transcription	Brain Angular Gyrus	brain
31	chr3:51388800-51390200	Weak transcription	Fetal Brain Female	brain
32	chr3:51389000-51391800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:51389000-51392600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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