Variant report

Variant	rs4604725
Chromosome Location	chr1:197365105-197365106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10922231	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]
rs10922236	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs10922260	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1135810	0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap]
rs12042609	0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs1337166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1345529	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs1923759	0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4026514	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4147323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap]
rs4274099	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4418639	0.86[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs4915545	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7534863	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs927510	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787082	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs993487	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4604725	LHX2	trans	parietal	SCAN
rs4604725	DENND1B	cis	parietal	SCAN
rs4604725	ZFP3	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197354400-197366000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197361400-197368800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:197362400-197368800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:197364600-197365200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr1:197364800-197370800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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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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