Variant report

Variant	rs162490
Chromosome Location	chr21:28310740-28310741
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1497288	1.00[ASN][1000 genomes]
rs151056	0.91[EUR][1000 genomes]
rs151059	0.84[EUR][1000 genomes]
rs162488	0.87[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162491	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162492	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162493	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162494	0.84[EUR][1000 genomes]
rs162496	0.88[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs162497	0.88[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs162498	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162499	0.88[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs162501	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs162503	1.00[ASN][1000 genomes]
rs162504	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162505	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162506	0.87[GIH][hapmap];0.85[YRI][hapmap]
rs162507	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162508	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162510	1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162516	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162520	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162521	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162531	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162532	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs162533	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162534	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162535	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162536	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162537	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162538	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162539	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162540	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162541	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229045	0.91[EUR][1000 genomes]
rs229046	0.91[EUR][1000 genomes]
rs229049	0.84[EUR][1000 genomes]
rs229050	0.84[EUR][1000 genomes]
rs229053	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs229060	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229061	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229063	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229064	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229069	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229071	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229076	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229078	0.82[ASW][hapmap];0.87[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229079	0.83[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs229085	1.00[ASN][1000 genomes]
rs229087	0.91[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229088	0.91[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229089	0.91[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs229090	0.91[EUR][1000 genomes]
rs229091	0.96[CEU][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs229093	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229095	0.87[CEU][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229097	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229103	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229109	0.87[EUR][1000 genomes]
rs229110	0.85[EUR][1000 genomes]
rs233897	0.85[EUR][1000 genomes]
rs233898	0.85[EUR][1000 genomes]
rs233899	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs233900	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830556	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830584	0.91[EUR][1000 genomes]
rs2830589	0.84[EUR][1000 genomes]
rs389125	0.87[EUR][1000 genomes]
rs431134	0.89[EUR][1000 genomes]
rs457947	1.00[ASN][1000 genomes]
rs4817147	1.00[ASN][1000 genomes]
rs7281968	0.91[EUR][1000 genomes]
rs73358063	1.00[ASN][1000 genomes]
rs73358075	1.00[ASN][1000 genomes]
rs73899348	1.00[ASN][1000 genomes]
rs8127064	1.00[ASN][1000 genomes]
rs8131204	1.00[ASN][1000 genomes]
rs8992	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9647124	1.00[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

No data

Chromatin state (count:38 , 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	chr21:28294600-28318000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr21:28294600-28318200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr21:28295400-28318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr21:28296600-28315400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:28296800-28318200	Weak transcription	Left Ventricle	heart
9	chr21:28297000-28311800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr21:28298600-28311600	Weak transcription	Brain Germinal Matrix	brain
11	chr21:28298600-28313000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr21:28298800-28311000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:28298800-28318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr21:28300200-28311200	Weak transcription	NHLF	lung
15	chr21:28301800-28313000	Strong transcription	HSMMtube	muscle
16	chr21:28305800-28319200	Weak transcription	Placenta	Placenta
17	chr21:28306600-28311800	Weak transcription	Osteobl	bone
18	chr21:28306600-28333600	Weak transcription	Fetal Intestine Large	intestine
19	chr21:28307200-28311800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr21:28307200-28312200	Weak transcription	Fetal Intestine Small	intestine
21	chr21:28307400-28311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr21:28307400-28318200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr21:28307400-28318200	Weak transcription	Fetal Stomach	stomach
24	chr21:28307600-28324800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr21:28308400-28310800	Weak transcription	Fetal Muscle Leg	muscle
26	chr21:28308600-28310800	Weak transcription	Ovary	ovary
27	chr21:28308600-28311200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr21:28308600-28311200	Weak transcription	Colon Smooth Muscle	Colon
29	chr21:28308800-28311200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr21:28308800-28311200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr21:28308800-28312000	Weak transcription	Fetal Kidney	kidney
32	chr21:28309600-28311200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr21:28309600-28337200	Weak transcription	Fetal Heart	heart
34	chr21:28309800-28311200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr21:28309800-28311200	Weak transcription	Fetal Lung	lung
36	chr21:28310000-28311400	Weak transcription	Adipose Nuclei	Adipose
37	chr21:28310200-28311200	Weak transcription	NHDF-Ad	bronchial
38	chr21:28310600-28313200	Enhancers	Liver	Liver

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