Variant report

Variant	rs2160017
Chromosome Location	chr7:147558570-147558571
allele	A/C
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:42)

rs_ID	r²[population]
rs1013335	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10233374	0.87[CHB][hapmap]
rs10233755	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10246256	0.91[CHB][hapmap]
rs1177007	0.86[CHB][hapmap];0.83[GIH][hapmap]
rs1186173	0.95[CHB][hapmap]
rs2247143	0.90[CHB][hapmap]
rs2373269	0.87[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.88[ASN][1000 genomes]
rs2373270	0.87[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2538974	0.87[CHB][hapmap]
rs2538979	0.87[CHB][hapmap]
rs2538983	0.82[CHB][hapmap]
rs2538988	0.87[CHB][hapmap]
rs2538989	0.87[CHB][hapmap]
rs2538990	0.82[CHB][hapmap]
rs2538992	0.82[CHB][hapmap]
rs2538994	0.82[CHB][hapmap]
rs2708238	0.87[CHB][hapmap]
rs2708239	0.87[CHB][hapmap]
rs2708240	0.82[CHB][hapmap]
rs2708243	0.85[CHB][hapmap]
rs2710102	0.87[CHB][hapmap]
rs2710105	0.80[CHB][hapmap]
rs2710108	0.82[CHB][hapmap]
rs2710139	0.87[CHB][hapmap]
rs2710140	0.87[CHB][hapmap]
rs2888536	0.87[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4140925	0.80[CHB][hapmap]
rs4305811	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs4308647	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4523170	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs4725747	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4726891	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4726892	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4726893	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955775	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs6958954	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6979332	0.96[CEU][hapmap];0.92[YRI][hapmap]
rs759177	0.87[CHB][hapmap]
rs759178	0.87[CHB][hapmap]
rs7794345	0.86[CHB][hapmap]
rs851715	0.91[CHB][hapmap];0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889397	chr7:147471710-147585819	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
2	nsv465193	chr7:147512619-147583680	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	nsv608965	chr7:147512619-147583680	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2160017	OR2F1	cis	cerebellum	SCAN
rs2160017	ANKRD44	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147557800-147558800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:147558000-147558600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr7:147558000-147558600	Enhancers	Brain Cingulate Gyrus	brain
4	chr7:147558000-147558600	Enhancers	Brain Hippocampus Middle	brain
5	chr7:147558000-147558600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr7:147558200-147558600	Enhancers	Brain Substantia Nigra	brain

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