Variant report

Variant	rs2830591
Chromosome Location	chr21:28316921-28316922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GABPA-19	chr21:28316887-28317423	NONHSAT081553
2	lnc-GABPA-19	chr21:28316887-28317399	l_2185_NR_027246

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10482979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700721	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13047132	0.93[EUR][1000 genomes]
rs13047248	0.94[EUR][1000 genomes]
rs13048083	0.94[EUR][1000 genomes]
rs13051983	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1444269	0.90[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs149415	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2017616	0.94[EUR][1000 genomes]
rs229053	1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2830578	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2830590	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3171407	0.95[EUR][1000 genomes]
rs34609314	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35197958	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36125779	0.94[EUR][1000 genomes]
rs3746836	0.90[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs62215996	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7283958	0.94[EUR][1000 genomes]
rs965135	0.85[AMR][1000 genomes];0.97[EUR][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
rs2830591	NCRNA00189	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28293000-28334800	Weak transcription	Hela-S3	cervix
2	chr21:28294600-28318000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr21:28294600-28318200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr21:28295400-28318200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr21:28296800-28318200	Weak transcription	Left Ventricle	heart
6	chr21:28298800-28318200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:28305800-28319200	Weak transcription	Placenta	Placenta
8	chr21:28306600-28333600	Weak transcription	Fetal Intestine Large	intestine
9	chr21:28307400-28318200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:28307400-28318200	Weak transcription	Fetal Stomach	stomach
11	chr21:28307600-28324800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr21:28309600-28337200	Weak transcription	Fetal Heart	heart
13	chr21:28312200-28318200	Weak transcription	Fetal Kidney	kidney
14	chr21:28312200-28318200	Weak transcription	Fetal Muscle Leg	muscle
15	chr21:28312200-28318200	Weak transcription	Psoas Muscle	Psoas
16	chr21:28312400-28318400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr21:28312600-28318200	Weak transcription	Fetal Lung	lung
18	chr21:28313000-28317200	Genic enhancers	HSMMtube	muscle
19	chr21:28313200-28318000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:28313200-28318000	Weak transcription	NHLF	lung
21	chr21:28313200-28318400	Weak transcription	Liver	Liver
22	chr21:28313600-28318200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr21:28313600-28319200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr21:28314400-28318000	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr21:28314600-28318200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr21:28314800-28320800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr21:28315000-28318000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr21:28315200-28317000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr21:28315200-28321000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr21:28315400-28318200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr21:28315600-28318000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:28315600-28318000	Weak transcription	Adipose Nuclei	Adipose
33	chr21:28315600-28320400	Strong transcription	Osteobl	bone
34	chr21:28315800-28317200	Strong transcription	HSMM	muscle
35	chr21:28315800-28318200	Weak transcription	Ovary	ovary
36	chr21:28316200-28317400	Enhancers	NHDF-Ad	bronchial
37	chr21:28316400-28318200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr21:28316800-28317000	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr21:28316800-28317400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast

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