Variant report

Variant	rs1541412
Chromosome Location	chr7:147712471-147712472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10240221	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs10249855	0.92[CEU][hapmap]
rs10808049	0.86[JPT][hapmap]
rs11771941	0.85[CHB][hapmap]
rs12532284	1.00[CEU][hapmap]
rs12532290	1.00[CEU][hapmap]
rs13237695	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17432092	0.92[CHB][hapmap]
rs17432209	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs1997530	0.81[CHB][hapmap]
rs2141954	0.81[CHB][hapmap]
rs2178771	0.86[CHB][hapmap]
rs2189883	0.93[CHB][hapmap];0.83[CHD][hapmap]
rs2204926	0.86[CHB][hapmap]
rs2214681	0.92[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs2214682	0.91[CHB][hapmap]
rs2527054	0.92[JPT][hapmap]
rs2707553	0.85[CHB][hapmap]
rs2707582	0.96[CEU][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2707585	0.81[CHB][hapmap]
rs2708248	0.85[CHB][hapmap]
rs2708284	0.86[CHB][hapmap]
rs2710082	0.86[CHB][hapmap]
rs2710157	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs2859687	0.93[CHB][hapmap]
rs4571659	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs4725757	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4725758	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4726903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4726912	0.85[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes]
rs4726918	0.82[EUR][1000 genomes]
rs6464849	0.87[EUR][1000 genomes]
rs66553749	0.80[ASN][1000 genomes]
rs6942912	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6946207	0.95[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6949561	0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6953539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969904	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6970083	0.85[AMR][1000 genomes]
rs8180832	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs961519	0.85[CHB][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes]
rs977284	1.00[CEU][hapmap]
rs993715	0.85[CHB][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv889399	chr7:147643923-147712471	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv889400	chr7:147650411-147712471	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1541412	OR2A12	cis	cerebellum	SCAN
rs1541412	CRYGN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147709200-147717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:147709600-147718400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr7:147711600-147716400	Enhancers	Fetal Lung	lung
4	chr7:147712400-147712600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:147712400-147713600	Enhancers	Placenta	Placenta

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