Variant report

Variant	rs2818222
Chromosome Location	chr13:54832320-54832321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12429973	0.82[AMR][1000 genomes]
rs12430260	0.86[ASN][1000 genomes]
rs17604306	0.86[ASN][1000 genomes]
rs17667588	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17667614	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2782502	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818223	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883886	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4883887	0.86[AMR][1000 genomes]
rs4884928	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57804893	0.86[ASN][1000 genomes]
rs682930	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs684299	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs795647	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs795649	0.86[AMR][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	esv3375545	chr13:54517432-54908108	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1051063	chr13:54777487-54997866	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv541778	chr13:54777487-54997866	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
4	nsv471132	chr13:54788842-54885744	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2818222	COL5A1	trans	lymphoblastoid	seeQTL
rs2818222	SYCP2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54822800-54835600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr13:54831200-54834000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr13:54831600-54832400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:54831800-54833400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr13:54831800-54835600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:54832200-54832600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr13:54832200-54839000	Enhancers	HUES64 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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