Variant report

Variant	rs7592227
Chromosome Location	chr2:186623388-186623389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1010838	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1010839	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1019428	0.83[AFR][1000 genomes]
rs1019429	0.81[TSI][hapmap]
rs1019430	0.83[AFR][1000 genomes]
rs10490390	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs10490391	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs10490392	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs10803994	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10931194	0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10931197	0.83[AFR][1000 genomes]
rs10931198	0.83[AFR][1000 genomes]
rs10931200	0.83[AFR][1000 genomes]
rs1119051	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11686997	0.83[AFR][1000 genomes]
rs11695215	0.83[AFR][1000 genomes]
rs11695263	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11883784	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs11884004	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11884071	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap]
rs11894788	0.85[YRI][hapmap]
rs11903585	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12053506	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12618129	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12622494	0.83[AFR][1000 genomes]
rs12623222	0.82[AFR][1000 genomes]
rs1544710	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes]
rs1544711	0.88[AFR][1000 genomes]
rs1544712	0.88[AFR][1000 genomes]
rs1544713	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17228146	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17228441	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17228483	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17229201	0.98[LWK][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs17229222	0.83[AFR][1000 genomes]
rs17813736	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17814545	0.86[YRI][hapmap]
rs1862066	0.83[AFR][1000 genomes]
rs1986166	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2161035	0.83[AFR][1000 genomes]
rs2161036	0.82[AFR][1000 genomes]
rs2287605	0.82[AFR][1000 genomes]
rs2287606	0.83[AFR][1000 genomes]
rs2370476	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2887761	0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2887762	0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs36004074	0.82[AFR][1000 genomes]
rs4547499	0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs55856163	0.88[AFR][1000 genomes]
rs55938253	0.83[AFR][1000 genomes]
rs58798964	0.83[AFR][1000 genomes]
rs60029104	0.83[AFR][1000 genomes]
rs6434141	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6434144	0.83[AFR][1000 genomes]
rs6705390	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6705753	0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6732973	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6733690	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6746722	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6759616	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67690898	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7424780	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7562137	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7566166	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7566901	0.85[YRI][hapmap]
rs7570827	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7574766	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7575226	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7584637	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7584776	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7587203	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7587685	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7592890	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs7605884	0.86[AFR][1000 genomes]
rs7608481	0.83[AFR][1000 genomes]
rs9646802	0.98[LWK][hapmap];0.97[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs992822	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007052	chr2:186441382-186864390	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv584019	chr2:186445393-186866874	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1009118	chr2:186450293-186864390	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008230	chr2:186474069-186818718	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv536076	chr2:186474069-186818718	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv584020	chr2:186475590-186661567	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv584021	chr2:186475590-186866841	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1796337	chr2:186618494-186704965	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1797599	chr2:186618494-186882821	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7592227	NCKAP1	cis	parietal	SCAN
rs7592227	FAM171B	cis	parietal	SCAN
rs7592227	FSIP2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:186606800-186632000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:186613600-186635000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:186622400-186625800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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