Variant report

Variant	rs11020424
Chromosome Location	chr11:93321185-93321186
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10160552	0.88[ASW][hapmap]
rs10831070	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831071	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831073	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10831078	0.83[ASN][1000 genomes]
rs11020446	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11020484	1.00[YRI][hapmap]
rs12791296	0.82[ASN][1000 genomes]
rs2155243	0.82[EUR][1000 genomes]
rs2212439	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4396249	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7105804	0.88[ASW][hapmap]
rs7123348	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7942374	0.91[AMR][1000 genomes];0.97[EUR][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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11020424	C11orf54	cis	cerebellum	SCAN
rs11020424	MED17	cis	cerebellum	SCAN
rs11020424	MED17	cis	parietal	SCAN
rs11020424	SCARNA9	cis	parietal	SCAN
rs11020424	SCARNA9	cis	cerebellum	SCAN
rs11020424	C11orf54	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93319200-93323200	Enhancers	Stomach Mucosa	stomach
2	chr11:93319400-93324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:93319600-93324400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:93320200-93321200	Enhancers	K562	blood
5	chr11:93320400-93322000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:93320400-93322400	Enhancers	Gastric	stomach
7	chr11:93320400-93322800	Enhancers	HepG2	liver
8	chr11:93320400-93324400	Weak transcription	A549	lung
9	chr11:93320600-93323400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr11:93320800-93321600	Enhancers	Pancreas	Pancrea
11	chr11:93321000-93321600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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