Variant report

Variant	rs1920193
Chromosome Location	chr3:116168964-116168965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1713001	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1713007	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1731597	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1731598	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731601	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1731610	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1795249	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795263	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2864815	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2902853	0.92[CEU][hapmap];0.81[CHD][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs3866148	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626095	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs4831140	0.97[AFR][1000 genomes];0.98[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	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1920193	IQCB1	cis	parietal	SCAN
rs1920193	STXBP5L	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116164200-116169800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:116165400-116169400	Weak transcription	Brain Angular Gyrus	brain
3	chr3:116165600-116171600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:116167600-116171600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:116167800-116169400	Enhancers	Brain Substantia Nigra	brain
6	chr3:116168400-116169200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:116168400-116169800	Enhancers	Fetal Brain Male	brain
8	chr3:116168600-116169400	Enhancers	Fetal Lung	lung
9	chr3:116168800-116169400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:116168800-116171600	Weak transcription	Brain Anterior Caudate	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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