Variant report

Variant	rs2246593
Chromosome Location	chr1:160943839-160943840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1023115	0.80[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12030262	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs2243414	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2243415	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2243479	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246139	1.00[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2246170	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2246598	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249532	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2250288	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2256633	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2265241	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265328	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2265329	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2265330	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2369977	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2483143	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2483148	0.80[AMR][1000 genomes]
rs2988723	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6427562	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524408	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7546890	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]

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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2246593	OR10R2	cis	cerebellum	SCAN
rs2246593	MNDA	cis	cerebellum	SCAN
rs2246593	DARC	cis	parietal	SCAN
rs2246593	ARHGEF11	cis	cerebellum	SCAN
rs2246593	F11R	cis	parietal	SCAN
rs2246593	OR6N2	cis	parietal	SCAN
rs2246593	HDGF	cis	cerebellum	SCAN
rs2246593	USF1	cis	multi-tissue	Pritchard
rs2246593	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160942000-160944000	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr1:160942200-160944000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr1:160942200-160944400	Weak transcription	GM12878-XiMat	blood
4	chr1:160942800-160946200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:160943200-160951000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:160943200-160959800	Weak transcription	Pancreas	Pancrea
7	chr1:160943600-160949200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:160943800-160950600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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