Variant report

Variant	rs2461822
Chromosome Location	chr3:119520165-119520166
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12492296	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059232	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091204	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1357459	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1403526	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2461817	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2461818	0.89[LWK][hapmap];1.00[YRI][hapmap]
rs2461821	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2461823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2472677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4440154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688040	0.85[ASN][1000 genomes]
rs55764158	0.95[ASN][1000 genomes]
rs62264683	0.82[AFR][1000 genomes]
rs6438549	0.89[LWK][hapmap];1.00[YRI][hapmap]
rs6771638	0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs6772976	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2461822	CCDC58	cis	cerebellum	SCAN
rs2461822	PTPLB	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119514400-119526800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119515000-119526000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:119515400-119526000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:119515400-119527200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:119515400-119528600	Weak transcription	Colonic Mucosa	Colon
6	chr3:119515800-119527400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:119516800-119520600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:119516800-119534600	Weak transcription	HepG2	liver
9	chr3:119519800-119521400	Enhancers	Liver	Liver
10	chr3:119520000-119520200	Weak transcription	Fetal Intestine Small	intestine

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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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