Variant report

Variant	rs16866000
Chromosome Location	chr2:178873453-178873454
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1020010	0.81[ASW][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap]
rs10201731	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1025598	0.83[CHD][hapmap]
rs10497480	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11899873	0.83[ASN][1000 genomes]
rs12472886	0.93[YRI][hapmap]
rs12473461	0.92[YRI][hapmap]
rs12477170	0.91[YRI][hapmap]
rs12478277	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs12618253	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618606	0.89[YRI][hapmap]
rs12621562	0.81[ASW][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap]
rs1405648	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1527286	0.93[YRI][hapmap]
rs1527287	0.93[YRI][hapmap]
rs1527293	0.93[YRI][hapmap]
rs1527294	0.91[YRI][hapmap]
rs1527295	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs1527296	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs1534289	0.93[YRI][hapmap]
rs1546813	0.93[YRI][hapmap]
rs1554776	0.92[YRI][hapmap]
rs16866025	0.83[CHD][hapmap]
rs16866032	0.83[CHD][hapmap]
rs17329531	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs17330075	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17401986	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17636610	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs17687590	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs1830209	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs1836672	0.93[YRI][hapmap]
rs1852497	0.93[YRI][hapmap]
rs1898587	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1982131	0.93[YRI][hapmap]
rs2043547	0.92[YRI][hapmap]
rs2060490	0.93[YRI][hapmap]
rs2117738	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs2117740	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs2365899	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2695742	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3108451	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs4335982	0.93[YRI][hapmap]
rs4468852	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4893844	0.93[YRI][hapmap]
rs4893994	0.93[YRI][hapmap]
rs4893995	0.92[YRI][hapmap]
rs55841094	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60047236	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6716206	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6726809	0.91[YRI][hapmap]
rs6738098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6750869	0.81[ASW][hapmap];0.93[YRI][hapmap]
rs6758442	0.92[YRI][hapmap]
rs744397	0.81[MKK][hapmap];0.93[YRI][hapmap]
rs744398	0.82[AFR][1000 genomes]
rs7570423	0.89[YRI][hapmap]
rs7570981	1.00[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs7588062	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7591800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7595479	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs934568	0.93[YRI][hapmap]
rs9679090	0.93[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv998304	chr2:178756380-178924378	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv536056	chr2:178756380-178924378	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16866000	SP3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178872200-178874000	Enhancers	Brain Germinal Matrix	brain
2	chr2:178873000-178873600	Enhancers	A549	lung
3	chr2:178873000-178873800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:178873000-178874000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:178873200-178873600	Enhancers	Brain Angular Gyrus	brain
6	chr2:178873200-178874000	Enhancers	Fetal Brain Male	brain
7	chr2:178873400-178873600	Enhancers	Pancreas	Pancrea
8	chr2:178873400-178873800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:178873400-178873800	Enhancers	Fetal Brain Female	brain
10	chr2:178873400-178873800	Enhancers	NH-A	brain

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