Variant report

Variant	rs9305590
Chromosome Location	chr21:37910446-37910447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLCS-2	chr21:37909493-37910751	l_2208_chr21:37904790-37910751_brain

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11909578	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13046506	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13047871	0.82[AMR][1000 genomes]
rs13049189	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13049736	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1892908	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1892909	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2015187	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2187304	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2835382	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2835383	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2835388	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2835389	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2835390	0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs377483	0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs377777	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs412510	0.82[YRI][hapmap]
rs450932	0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4817806	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4817807	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4817808	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6517361	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs70940557	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8128229	0.86[EUR][1000 genomes]
rs914148	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9305591	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9305592	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9305594	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9305595	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9653721	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9980855	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9981041	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834090	chr21:37812545-38009542	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1064290	chr21:37878964-37983133	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3384461	chr21:37910382-37913780	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:37897000-37911600	Weak transcription	Pancreas	Pancrea
2	chr21:37908000-37911800	Weak transcription	Gastric	stomach
3	chr21:37908400-37911600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:37908400-37911800	Weak transcription	Fetal Kidney	kidney
5	chr21:37908800-37911000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:37909400-37914400	Weak transcription	Placenta	Placenta
7	chr21:37910400-37910600	Flanking Active TSS	GM12878-XiMat	blood

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