Variant report

Variant	rs534100
Chromosome Location	chr2:21321158-21321159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs312942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs312947	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs312948	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312949	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs312950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs312951	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs312952	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs312954	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs312955	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs312956	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs312957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs312959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs312962	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs312963	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs312971	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs312972	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs312973	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs312975	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs312977	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs312978	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs563476	0.89[AFR][1000 genomes]
rs575905	0.88[AFR][1000 genomes]
rs581998	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645456	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs675430	0.89[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873728	chr2:21250914-21460786	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs534100	MSGN1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:21315800-21326400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:21318200-21322800	Enhancers	Fetal Intestine Large	intestine
3	chr2:21318200-21323600	Enhancers	Fetal Intestine Small	intestine
4	chr2:21318400-21322400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:21320400-21321200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr2:21320400-21321600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:21320400-21321800	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:21320400-21322400	Enhancers	Adipose Nuclei	Adipose
9	chr2:21320600-21321200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr2:21320600-21322600	Enhancers	HepG2	liver
11	chr2:21320800-21321400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:21320800-21326200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:21321000-21321400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr2:21321000-21321400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr2:21321000-21321800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr2:21321000-21323200	Enhancers	Liver	Liver

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