Variant report

Variant	rs2838464
Chromosome Location	chr21:45421079-45421080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45419334..45421433-chr21:45476805..45478388,2	K562	blood:
2	chr21:45418408..45422814-chr21:45429563..45432398,4	MCF-7	breast:
3	chr21:45418903..45427442-chr21:45428252..45434057,14	K562	blood:
4	chr21:45419220..45421707-chr21:45432481..45434970,2	MCF-7	breast:
5	chr21:45409643..45411374-chr21:45420843..45423810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160218	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1051981	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs13048791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13049059	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13052507	0.82[ASN][1000 genomes]
rs17004630	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2006694	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2071154	1.00[JPT][hapmap]
rs2187313	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2255828	0.85[TSI][hapmap]
rs2255955	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2276532	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2277805	0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2299816	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2299817	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2838469	0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs2838486	0.85[TSI][hapmap]
rs2838507	0.85[JPT][hapmap]
rs2838508	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2838509	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2850154	0.93[JPT][hapmap]
rs3788104	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3788108	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs4818886	0.81[CHB][hapmap]
rs4819361	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4819362	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4819375	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs58008499	1.00[ASN][1000 genomes]
rs62229731	0.91[ASN][1000 genomes]
rs62229732	0.94[ASN][1000 genomes]
rs62229733	0.94[ASN][1000 genomes]
rs62229734	0.97[ASN][1000 genomes]
rs62229738	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7277731	0.92[ASN][1000 genomes]
rs7282324	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7676	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs8131617	0.99[ASN][1000 genomes]
rs885872	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs965733	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs968713	1.00[JPT][hapmap]
rs9985064	0.81[CHB][hapmap];0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv913888	chr21:45351206-45428278	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1063752	chr21:45406095-45460342	Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv459293	chr21:45415913-45555079	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv587721	chr21:45415913-45555079	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2838464	ABCG1	cis	parietal	SCAN
rs2838464	ABCG1	cis	cerebellum	SCAN
rs2838464	PWP2	cis	parietal	SCAN
rs2838464	C21orf129	cis	cerebellum	SCAN
rs2838464	PWP2	Cis_1M	lymphoblastoid	RTeQTL
rs2838464	TRAPPC10	cis	cerebellum	SCAN
rs2838464	C21orf33	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45418200-45421800	Enhancers	Brain Hippocampus Middle	brain
2	chr21:45418800-45421600	Enhancers	Brain Substantia Nigra	brain
3	chr21:45419000-45421400	Enhancers	Brain Cingulate Gyrus	brain
4	chr21:45419000-45421600	Enhancers	Brain Angular Gyrus	brain
5	chr21:45419000-45421800	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr21:45419400-45421600	Enhancers	Brain Anterior Caudate	brain
7	chr21:45420200-45421600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr21:45420600-45425400	Weak transcription	HSMM	muscle
9	chr21:45420800-45421400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:45420800-45425200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr21:45421000-45422000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr21:45421000-45425400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr21:45421000-45425600	Weak transcription	HSMMtube	muscle

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