Variant report

Variant	rs229079
Chromosome Location	chr21:28298049-28298050
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs151056	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs151059	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162488	0.82[EUR][1000 genomes]
rs162490	0.83[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs162491	0.82[EUR][1000 genomes]
rs162492	0.82[EUR][1000 genomes]
rs162493	0.82[EUR][1000 genomes]
rs162494	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs162496	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs162497	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs162498	0.87[CEU][hapmap];0.82[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs162499	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]
rs162510	0.82[GIH][hapmap];0.88[TSI][hapmap]
rs162516	0.91[EUR][1000 genomes]
rs162520	0.91[EUR][1000 genomes]
rs162521	0.91[EUR][1000 genomes]
rs162531	0.89[EUR][1000 genomes]
rs162532	0.89[EUR][1000 genomes]
rs162533	0.89[EUR][1000 genomes]
rs162534	0.88[EUR][1000 genomes]
rs162535	0.89[EUR][1000 genomes]
rs162536	0.89[EUR][1000 genomes]
rs162537	0.89[EUR][1000 genomes]
rs162538	0.87[EUR][1000 genomes]
rs162539	0.86[EUR][1000 genomes]
rs162540	0.86[EUR][1000 genomes]
rs162541	0.86[EUR][1000 genomes]
rs16979458	0.81[CHD][hapmap]
rs229045	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229046	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229049	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229050	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs229060	0.91[EUR][1000 genomes]
rs229061	0.91[EUR][1000 genomes]
rs229063	0.91[EUR][1000 genomes]
rs229064	0.91[EUR][1000 genomes]
rs229069	0.90[EUR][1000 genomes]
rs229071	0.91[EUR][1000 genomes]
rs229076	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs229078	0.87[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs229087	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs229088	0.92[CEU][hapmap];0.85[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs229089	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs229090	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs229091	0.87[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs229093	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs229095	0.88[CEU][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs229097	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs229109	0.84[EUR][1000 genomes]
rs229110	0.80[EUR][1000 genomes]
rs2298657	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs233897	0.89[EUR][1000 genomes]
rs233898	0.89[EUR][1000 genomes]
rs233899	0.83[EUR][1000 genomes]
rs233900	0.83[EUR][1000 genomes]
rs2830556	0.80[EUR][1000 genomes]
rs2830584	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2830589	0.87[CEU][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs389125	0.84[EUR][1000 genomes]
rs431134	0.85[EUR][1000 genomes]
rs438349	0.85[JPT][hapmap]
rs56153501	0.99[ASN][1000 genomes]
rs7281968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1067026	chr21:28282660-28298049	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs229079	MRPL39	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr21:28291400-28299400	Weak transcription	NHLF	lung
3	chr21:28291600-28312200	Strong transcription	HSMM	muscle
4	chr21:28292800-28298400	Weak transcription	Pancreas	Pancrea
5	chr21:28293000-28334800	Weak transcription	Hela-S3	cervix
6	chr21:28293800-28298200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr21:28293800-28303600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr21:28294600-28305800	Weak transcription	Small Intestine	intestine
9	chr21:28294600-28318000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr21:28294600-28318200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr21:28294800-28307200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr21:28295000-28303600	Weak transcription	Fetal Intestine Small	intestine
13	chr21:28295200-28306600	Strong transcription	Osteobl	bone
14	chr21:28295200-28310000	Strong transcription	Adipose Nuclei	Adipose
15	chr21:28295400-28300400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr21:28295400-28318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr21:28295600-28300600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr21:28295800-28300400	Strong transcription	Fetal Muscle Leg	muscle
19	chr21:28296200-28307800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr21:28296600-28300400	Strong transcription	HSMMtube	muscle
21	chr21:28296600-28302200	Weak transcription	Esophagus	oesophagus
22	chr21:28296600-28315400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr21:28296800-28298400	Weak transcription	Fetal Stomach	stomach
24	chr21:28296800-28304000	Weak transcription	Fetal Intestine Large	intestine
25	chr21:28296800-28304200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr21:28296800-28305000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr21:28296800-28307400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr21:28296800-28308200	Weak transcription	Fetal Lung	lung
29	chr21:28296800-28318200	Weak transcription	Left Ventricle	heart
30	chr21:28297000-28299200	Weak transcription	Fetal Kidney	kidney
31	chr21:28297000-28299400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr21:28297000-28299400	Weak transcription	NHDF-Ad	bronchial
33	chr21:28297000-28299600	Weak transcription	Spleen	Spleen
34	chr21:28297000-28311800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr21:28297200-28298600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr21:28297200-28298600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr21:28297200-28298600	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr21:28297400-28298600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr21:28297600-28298200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr21:28297600-28298400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr21:28297800-28298200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr21:28297800-28298600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr21:28297800-28298800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr21:28297800-28299200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr21:28297800-28308200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr21:28298000-28298200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr21:28298000-28298600	Enhancers	H1 Cell Line	embryonic stem cell
48	chr21:28298000-28298600	Enhancers	H9 Cell Line	embryonic stem cell
49	chr21:28298000-28298600	Genic enhancers	Ovary	ovary
50	chr21:28298000-28298800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links