Variant report

Variant	rs4526780
Chromosome Location	chr11:120730621-120730622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10892628	0.88[AMR][1000 genomes]
rs10892629	0.81[ASW][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11600004	0.90[AMR][1000 genomes]
rs11601867	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11606105	0.90[AMR][1000 genomes]
rs11607580	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11608113	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55966937	0.86[AMR][1000 genomes]
rs7103097	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7105258	1.00[ASN][1000 genomes]
rs7123228	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003760	0.86[AMR][1000 genomes]
rs73578569	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1038264	chr11:120582595-120799335	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv541181	chr11:120582595-120799335	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832286	chr11:120585843-120745846	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4526780	TRAPPC4	cis	parietal	SCAN
rs4526780	OR10G7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120704400-120746000	Weak transcription	Brain Hippocampus Middle	brain
2	chr11:120704400-120748800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:120714400-120746600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:120715400-120745000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:120728800-120733000	Weak transcription	Brain Anterior Caudate	brain
6	chr11:120729200-120730800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr11:120729200-120751200	Weak transcription	Ovary	ovary
8	chr11:120729600-120731000	Enhancers	Placenta	Placenta
9	chr11:120730000-120730800	Enhancers	Left Ventricle	heart
10	chr11:120730000-120733600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:120730000-120746600	Weak transcription	Fetal Lung	lung
12	chr11:120730200-120730800	Enhancers	Lung	lung
13	chr11:120730200-120731000	Enhancers	Right Atrium	heart
14	chr11:120730200-120737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:120730600-120730800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:120730600-120730800	Enhancers	iPS DF 19.11 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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