Variant report

Variant	rs1469973
Chromosome Location	chr2:178563430-178563431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1004541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004542	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175364	0.82[CHB][hapmap]
rs10192481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10930805	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11677821	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11684634	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs12622125	0.82[CHB][hapmap]
rs12987101	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs12989020	1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs13012431	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs13428806	0.82[CHB][hapmap]
rs1344917	0.83[AMR][1000 genomes]
rs1344925	0.82[MEX][hapmap]
rs1347731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370662	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370663	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370664	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438037	0.80[AMR][1000 genomes]
rs1438038	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs1438039	0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs1438048	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs1438054	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1438055	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1469972	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561315	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1561319	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs1561320	0.82[CHB][hapmap]
rs16865645	0.89[JPT][hapmap]
rs16865726	0.83[AMR][1000 genomes]
rs17400512	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1866208	0.82[CHB][hapmap]
rs1866209	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs1866210	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs1866211	0.80[AMR][1000 genomes]
rs1866212	0.80[AMR][1000 genomes]
rs1975321	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975322	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975324	0.80[AMR][1000 genomes]
rs2033760	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164857	0.82[CHB][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs2164860	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365889	0.80[AMR][1000 genomes]
rs2886424	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2886498	0.82[CHB][hapmap];0.80[AMR][1000 genomes]
rs3731809	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754991	0.82[CHB][hapmap]
rs3754993	0.82[CHB][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs3754994	0.80[AMR][1000 genomes]
rs3770023	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770034	0.82[CHB][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes]
rs4893839	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs4893840	0.82[CHB][hapmap]
rs4893980	0.91[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4893981	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4893982	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4893984	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4893985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893987	0.82[CHB][hapmap]
rs6433693	0.80[AMR][1000 genomes]
rs6718702	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739583	1.00[JPT][hapmap]
rs6756240	0.82[CHB][hapmap]
rs6760930	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749207	0.82[CHB][hapmap]
rs749208	0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs7596360	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs934809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998059	0.82[CHB][hapmap];0.82[MEX][hapmap]
rs999218	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv431812	chr2:178525371-178584470	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007925	chr2:178535922-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv870023	chr2:178545623-178581407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv2762967	chr2:178546919-178577002	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1005991	chr2:178550049-178577002	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv528219	chr2:178551924-178567151	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1003983	chr2:178551958-178577002	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	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
rs1469973	SP3	cis	parietal	SCAN
rs1469973	TTC30A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178558200-178576600	Weak transcription	Pancreas	Pancrea
2	chr2:178559000-178563600	Weak transcription	Ovary	ovary
3	chr2:178563000-178574800	Weak transcription	Fetal Muscle Leg	muscle

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