Variant report

Variant	rs7127374
Chromosome Location	chr11:84620936-84620937
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:13)

rs_ID	r²[population]
rs10792787	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792788	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10898326	0.88[MEX][hapmap]
rs10898330	0.88[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898331	0.94[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10898332	0.87[ASN][1000 genomes]
rs11234243	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12225342	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1940126	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34083949	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4943904	0.89[AMR][1000 genomes]
rs55872437	0.94[ASN][1000 genomes]
rs7111775	0.94[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv948410	chr11:83918339-84812001	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1045974	chr11:84187214-84708462	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1048051	chr11:84419442-84784233	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv541109	chr11:84419442-84784233	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv817205	chr11:84497319-84628963	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv555625	chr11:84547441-84629013	Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7127374	SYTL2	cis	cerebellum	SCAN
rs7127374	C11orf73	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:84620200-84621400	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr11:84620600-84621000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr11:84620600-84621200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr11:84620600-84621200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:84620600-84621200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:84620600-84621200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr11:84620600-84621200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr11:84620600-84621400	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr11:84620800-84621200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:84620800-84621200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:84620800-84621200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr11:84620800-84621200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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

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