Variant report

Variant	rs325863
Chromosome Location	chr5:41049389-41049390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10041397	0.84[ASN][1000 genomes]
rs10512764	0.84[CHB][hapmap];0.81[GIH][hapmap]
rs1423395	0.83[ASN][1000 genomes]
rs167815	0.83[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs170529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs325853	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.91[YRI][hapmap]
rs325854	0.82[CHB][hapmap]
rs325856	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325857	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs325858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs325859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs325860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs325864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325866	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325870	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325871	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs325872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs325873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs325876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3805715	0.89[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap]
rs387699	0.82[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.91[MKK][hapmap];0.81[YRI][hapmap]
rs391243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs56909233	0.83[ASN][1000 genomes]
rs618334	0.83[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs644800	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs648563	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs67738881	0.83[ASN][1000 genomes]
rs865093	0.83[ASW][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.85[LWK][hapmap];0.94[MKK][hapmap];0.87[YRI][hapmap]
rs918608	0.82[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830268	chr5:40897361-41138366	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs325863	C9	cis	parietal	SCAN
rs325863	GALNT9	trans	lymphoblastoid	seeQTL
rs325863	LHX2	trans	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41049200-41049400	Enhancers	Liver	Liver
2	chr5:41049200-41049800	Enhancers	Small Intestine	intestine
3	chr5:41049200-41050000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:41049200-41050000	Enhancers	Gastric	stomach
5	chr5:41049200-41050000	Enhancers	Ovary	ovary
6	chr5:41049200-41050200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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