Variant report

Variant	rs162499
Chromosome Location	chr21:28305647-28305648
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs151056	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151057	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs151059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162487	0.87[ASN][1000 genomes]
rs162488	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs162490	0.88[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs162491	0.85[EUR][1000 genomes]
rs162492	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs162493	0.85[EUR][1000 genomes]
rs162494	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs162496	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162497	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[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162498	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs162510	0.88[TSI][hapmap]
rs162516	0.87[EUR][1000 genomes]
rs162520	0.87[EUR][1000 genomes]
rs162521	0.87[EUR][1000 genomes]
rs162531	0.86[EUR][1000 genomes]
rs162532	0.86[EUR][1000 genomes]
rs162533	0.86[EUR][1000 genomes]
rs162534	0.85[EUR][1000 genomes]
rs162535	0.86[EUR][1000 genomes]
rs162536	0.86[EUR][1000 genomes]
rs162537	0.86[EUR][1000 genomes]
rs162538	0.84[EUR][1000 genomes]
rs162539	0.83[EUR][1000 genomes]
rs162540	0.83[EUR][1000 genomes]
rs162541	0.83[EUR][1000 genomes]
rs16979458	0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs170655	0.87[ASN][1000 genomes]
rs229045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229046	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229049	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs229050	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs229051	0.87[ASN][1000 genomes]
rs229060	0.87[EUR][1000 genomes]
rs229061	0.87[EUR][1000 genomes]
rs229063	0.87[EUR][1000 genomes]
rs229064	0.87[EUR][1000 genomes]
rs229069	0.87[EUR][1000 genomes]
rs229071	0.87[EUR][1000 genomes]
rs229076	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs229078	0.83[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs229079	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229087	0.88[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs229088	0.88[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs229089	0.88[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs229090	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs229091	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs229093	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs229095	0.84[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs229097	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs229109	0.81[EUR][1000 genomes]
rs2298657	0.81[CHD][hapmap]
rs233896	0.81[GIH][hapmap]
rs233897	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233898	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs233899	0.84[EUR][1000 genomes]
rs233900	0.84[EUR][1000 genomes]
rs2830584	0.93[CHB][hapmap];0.86[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2830588	0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2830589	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs389125	0.81[EUR][1000 genomes]
rs431134	0.82[EUR][1000 genomes]
rs438349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7281968	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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	nsv1066573	chr21:28096356-28374354	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1057400	chr21:28104936-28359948	Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv834068	chr21:28179670-28360808	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs162499	MRPL39	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28291000-28311800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr21:28291600-28312200	Strong transcription	HSMM	muscle
3	chr21:28293000-28334800	Weak transcription	Hela-S3	cervix
4	chr21:28294600-28305800	Weak transcription	Small Intestine	intestine
5	chr21:28294600-28318000	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr21:28294600-28318200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr21:28294800-28307200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr21:28295200-28306600	Strong transcription	Osteobl	bone
9	chr21:28295200-28310000	Strong transcription	Adipose Nuclei	Adipose
10	chr21:28295400-28318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr21:28296200-28307800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr21:28296600-28315400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr21:28296800-28307400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr21:28296800-28308200	Weak transcription	Fetal Lung	lung
15	chr21:28296800-28318200	Weak transcription	Left Ventricle	heart
16	chr21:28297000-28311800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr21:28297800-28308200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr21:28298600-28311600	Weak transcription	Brain Germinal Matrix	brain
19	chr21:28298600-28313000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:28298800-28311000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr21:28298800-28318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr21:28300200-28311200	Weak transcription	NHLF	lung
23	chr21:28301200-28309800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr21:28301400-28307600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr21:28301400-28308200	Strong transcription	NHDF-Ad	bronchial
26	chr21:28301800-28308400	Strong transcription	Fetal Kidney	kidney
27	chr21:28301800-28313000	Strong transcription	HSMMtube	muscle
28	chr21:28303600-28305800	Strong transcription	Fetal Stomach	stomach
29	chr21:28303600-28308400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:28304000-28305800	Strong transcription	Placenta	Placenta
31	chr21:28304000-28306600	Strong transcription	Fetal Intestine Large	intestine
32	chr21:28304000-28308400	Strong transcription	Fetal Muscle Leg	muscle
33	chr21:28304200-28306000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr21:28304200-28307400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr21:28304200-28307400	Strong transcription	Ovary	ovary
36	chr21:28304600-28308000	Weak transcription	Fetal Brain Male	brain
37	chr21:28304800-28305800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr21:28305000-28307400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr21:28305400-28306800	Weak transcription	Fetal Intestine Small	intestine
40	chr21:28305400-28307800	Weak transcription	Primary monocytes fromperipheralblood	blood

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