Variant report

Variant	rs10922231
Chromosome Location	chr1:197412976-197412977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10922236	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10922260	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1135810	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs12042609	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs1337166	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1345529	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs1923759	0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs2111930	0.81[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4026514	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4147323	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs4274099	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4418639	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4604725	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4915545	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534863	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs927510	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9787082	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs993487	0.97[EUR][1000 genomes];0.95[ASN][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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10922231	DENND1B	cis	parietal	SCAN
rs10922231	LHX2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197403800-197413000	Weak transcription	Brain Hippocampus Middle	brain
2	chr1:197407600-197414200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:197407800-197413800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:197409800-197414000	Weak transcription	Brain Anterior Caudate	brain
5	chr1:197410200-197414000	Weak transcription	Ovary	ovary
6	chr1:197410200-197417000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:197411400-197414000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:197411800-197432000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:197412000-197413600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:197412000-197433200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:197412200-197420200	Weak transcription	Hela-S3	cervix
12	chr1:197412600-197413800	Weak transcription	iPS-15b 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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