Variant report

Variant	rs1444269
Chromosome Location	chr21:28291455-28291456
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTS1-2	chr21:28290242-28292870	NONHSAT081552

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10482979	0.90[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs11700721	0.80[CEU][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs13047132	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13048083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13051983	0.91[EUR][1000 genomes]
rs149415	0.93[EUR][1000 genomes]
rs162512	0.98[ASN][1000 genomes]
rs162514	0.98[ASN][1000 genomes]
rs162515	0.98[ASN][1000 genomes]
rs162517	0.98[ASN][1000 genomes]
rs162518	0.98[ASN][1000 genomes]
rs162519	0.98[ASN][1000 genomes]
rs162522	0.98[ASN][1000 genomes]
rs162523	0.98[ASN][1000 genomes]
rs162524	0.93[ASN][1000 genomes]
rs162525	0.98[ASN][1000 genomes]
rs162526	0.95[ASN][1000 genomes]
rs162527	0.98[ASN][1000 genomes]
rs162528	0.98[ASN][1000 genomes]
rs162529	0.98[ASN][1000 genomes]
rs162530	0.98[ASN][1000 genomes]
rs16979423	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2017616	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs229059	0.98[ASN][1000 genomes]
rs229062	0.98[ASN][1000 genomes]
rs229066	0.98[ASN][1000 genomes]
rs229068	0.98[ASN][1000 genomes]
rs229072	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs229073	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.98[ASN][1000 genomes]
rs229074	0.87[ASN][1000 genomes]
rs2830578	0.92[EUR][1000 genomes]
rs2830582	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2830587	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2830590	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs2830591	0.90[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs3171407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34609314	0.95[EUR][1000 genomes]
rs35197958	0.96[EUR][1000 genomes]
rs35650435	0.98[ASN][1000 genomes]
rs36125779	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746836	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459804	0.98[ASN][1000 genomes]
rs62215996	0.95[EUR][1000 genomes]
rs7283958	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7510287	0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs965135	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1063371	chr21:28282660-28294991	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
6	nsv1065825	chr21:28282660-28296389	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
7	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
8	nsv1066904	chr21:28282834-28296389	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription 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
rs1444269	NCRNA00189	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28282400-28295000	Weak transcription	Fetal Kidney	kidney
2	chr21:28288600-28292400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr21:28289000-28293000	Enhancers	Hela-S3	cervix
4	chr21:28289600-28292400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr21:28289600-28295200	Weak transcription	Adipose Nuclei	Adipose
6	chr21:28289600-28296000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr21:28289600-28296000	Weak transcription	Ovary	ovary
8	chr21:28289600-28298000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr21:28289800-28295600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr21:28290600-28291600	Genic enhancers	HSMM	muscle
11	chr21:28290800-28291600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr21:28290800-28293200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr21:28290800-28293200	Enhancers	NHDF-Ad	bronchial
14	chr21:28290800-28296200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr21:28290800-28297200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr21:28291000-28291800	Genic enhancers	HSMMtube	muscle
17	chr21:28291000-28292600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr21:28291000-28293800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr21:28291000-28297600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr21:28291000-28297800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr21:28291000-28311800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr21:28291200-28295800	Weak transcription	Fetal Intestine Large	intestine
23	chr21:28291200-28297400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr21:28291400-28295200	Weak transcription	Osteobl	bone
25	chr21:28291400-28297600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr21:28291400-28299400	Weak transcription	NHLF	lung

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