Variant report

Variant	rs17661242
Chromosome Location	chr3:51472033-51472034
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10510757	0.94[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10510758	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12485610	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487426	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487468	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489219	0.83[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs12489414	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490471	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490889	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12491048	0.95[ASN][1000 genomes]
rs12492624	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493265	0.92[ASN][1000 genomes]
rs12493618	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493857	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493978	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494462	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12494979	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495561	0.82[CHB][hapmap]
rs13089799	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13090348	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370124	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17051783	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17051811	0.89[ASN][1000 genomes]
rs17712228	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1842394	0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2033703	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061949	0.88[MEX][hapmap]
rs2082992	0.93[ASN][1000 genomes]
rs2082993	0.92[ASN][1000 genomes]
rs2170177	0.83[CHD][hapmap];0.89[MEX][hapmap]
rs2217938	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241785	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304512	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2306430	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2306431	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356261	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2356298	0.94[ASN][1000 genomes]
rs35536327	0.89[ASN][1000 genomes]
rs3749317	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792408	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804766	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828395	1.00[ASW][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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468966	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687553	0.90[ASN][1000 genomes]
rs4687563	0.92[ASN][1000 genomes]
rs4687601	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687605	0.94[ASN][1000 genomes]
rs4687610	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687656	0.93[ASN][1000 genomes]
rs4687691	0.91[ASN][1000 genomes]
rs4687731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687777	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687794	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4687803	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687804	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687811	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687813	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974096	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974098	0.87[EUR][1000 genomes]
rs4974112	0.83[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]
rs55667499	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55671465	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56239081	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56729479	0.94[ASN][1000 genomes]
rs57027950	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57047724	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57603251	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57700326	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57831708	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58059174	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58189274	0.82[ASN][1000 genomes]
rs58201844	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58568178	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836277	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59563413	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59838596	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59953568	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60606339	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61233013	0.91[ASN][1000 genomes]
rs61419317	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61689323	0.92[ASN][1000 genomes]
rs72945708	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72945713	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72951443	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73834252	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73834253	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834254	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834258	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73837439	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73837442	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73837443	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751076	0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7642698	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs880478	0.89[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9817077	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9817872	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9819195	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9820140	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827186	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9829057	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9842600	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9843583	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9856134	0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9861019	0.88[ASN][1000 genomes]
rs9878592	0.83[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17661242	MAPKAPK3	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
2	chr3:51434000-51475600	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:51451200-51476800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:51458000-51474800	Weak transcription	K562	blood
11	chr3:51458200-51474400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:51458200-51474600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:51458200-51475200	Weak transcription	NHLF	lung
14	chr3:51458200-51475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:51458200-51477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:51458200-51478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:51458200-51489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
19	chr3:51458400-51473000	Weak transcription	Pancreas	Pancrea
20	chr3:51458400-51474200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:51458400-51475400	Weak transcription	Gastric	stomach
22	chr3:51458400-51500200	Weak transcription	Psoas Muscle	Psoas
23	chr3:51458800-51503800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:51460000-51472400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:51460000-51475400	Weak transcription	Aorta	Aorta
26	chr3:51460200-51474000	Weak transcription	A549	lung
27	chr3:51461800-51478000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:51462400-51478200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:51462600-51476000	Strong transcription	Primary T cells from cord blood	blood
30	chr3:51462600-51477000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:51462600-51477200	Strong transcription	Placenta	Placenta
32	chr3:51462600-51477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:51462600-51477400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr3:51462800-51475400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:51463000-51477200	Strong transcription	Liver	Liver
36	chr3:51463000-51477600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:51463200-51478000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:51463400-51478200	Strong transcription	Dnd41	blood
39	chr3:51463600-51477200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:51464000-51475400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr3:51464400-51476400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:51465000-51473000	Weak transcription	Osteobl	bone
43	chr3:51466800-51473000	Weak transcription	Esophagus	oesophagus
44	chr3:51466800-51473000	Weak transcription	Spleen	Spleen
45	chr3:51467000-51474000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:51467000-51474000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:51467000-51475000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:51467000-51475400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:51467600-51473000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:51467600-51474000	Weak transcription	Brain Substantia Nigra	brain

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