Variant report

Variant	rs948851
Chromosome Location	chr11:56955091-56955092
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10792077	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11603194	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11603531	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604352	0.81[ASN][1000 genomes]
rs11820215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1893937	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2077190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3017577	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4442567	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4939113	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs514354	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs567766	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.96[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];0.82[ASN][1000 genomes]
rs609763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.96[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];0.83[ASN][1000 genomes]
rs622932	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs652068	0.82[CHB][hapmap]
rs664437	0.82[CHB][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]

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	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs948851	OR10AG1	cis	parietal	SCAN
rs948851	LRRC55	cis	parietal	SCAN
rs948851	OR4C15	cis	parietal	SCAN
rs948851	GTDC1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56948200-56959200	Weak transcription	Gastric	stomach
2	chr11:56948400-56959400	Weak transcription	Right Atrium	heart
3	chr11:56948600-56955400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:56949400-56962600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:56950200-56955200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:56950200-56960400	Weak transcription	Right Ventricle	heart
7	chr11:56950200-56969800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:56952600-56967000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:56953000-56958400	Strong transcription	Brain Germinal Matrix	brain
10	chr11:56953200-56958400	Weak transcription	Fetal Brain Male	brain
11	chr11:56954000-56957800	Strong transcription	Fetal Brain Female	brain
12	chr11:56954400-56958400	Weak transcription	Fetal Muscle Leg	muscle
13	chr11:56954800-56955200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr11:56954800-56955200	Strong transcription	Fetal Stomach	stomach
15	chr11:56955000-56956000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:56955000-56959400	Weak transcription	Lung	lung

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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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