Variant report

Variant	rs1026505
Chromosome Location	chr4:173790157-173790158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10004584	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs1116651	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1116652	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11935653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12512152	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13112941	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1350586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1459154	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1459155	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1459156	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17058964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17058973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17058981	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs17318218	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17318489	0.90[ASN][1000 genomes]
rs1824347	0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1903126	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947639	0.95[ASN][1000 genomes]
rs28718496	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34547986	0.90[ASN][1000 genomes]
rs35447014	0.95[ASN][1000 genomes]
rs6553659	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6818634	0.83[LWK][hapmap];0.90[MKK][hapmap]
rs6833917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6844018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660673	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7673435	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7691157	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs898197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9637709	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637710	0.97[ASN][1000 genomes]
rs9968432	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv3327952	chr4:173591786-173805861	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv881394	chr4:173757115-173847405	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	esv1004880	chr4:173779390-173790743	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1026505	GIP	trans	parietal	SCAN
rs1026505	VEGFC	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173787200-173790600	Weak transcription	Liver	Liver
2	chr4:173788800-173790200	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr4:173789000-173790800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:173789000-173790800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:173789200-173790200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:173789600-173790200	Enhancers	H9 Cell Line	embryonic stem cell
7	chr4:173789600-173790200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr4:173789800-173790200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr4:173789800-173790400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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