Variant report

Variant	rs1947960
Chromosome Location	chr8:85461359-85461360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1021852	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1021853	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1039520	1.00[ASN][1000 genomes]
rs10453097	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10504803	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10504805	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12114244	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1319379	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1320769	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320770	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13248532	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13250018	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13252091	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap]
rs13253537	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13255463	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs13256410	0.83[EUR][1000 genomes]
rs13257448	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13259587	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13261209	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13264793	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13265396	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13271249	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13275430	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1351223	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs1393990	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1479092	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1479093	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1479094	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs1479096	0.96[CEU][hapmap];0.95[JPT][hapmap]
rs1479098	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1503600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503601	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503602	0.84[EUR][1000 genomes]
rs1564314	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap]
rs1564315	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1564316	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1566791	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1566792	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs1824887	1.00[JPT][hapmap]
rs1847344	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994149	0.82[JPT][hapmap]
rs2046313	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061866	0.86[MEX][hapmap]
rs2127218	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2169922	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs28751114	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs317947	0.85[JPT][hapmap]
rs4739691	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4740014	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4740015	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4740016	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4740017	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4740018	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs4740019	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4740020	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4740021	0.89[EUR][1000 genomes]
rs4740022	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4740023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4740024	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60533047	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6473553	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6473554	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs6473555	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7010781	0.86[MEX][hapmap]
rs7011638	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7013087	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap]
rs711002	0.85[JPT][hapmap]
rs711006	0.85[JPT][hapmap]
rs711007	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs711011	1.00[JPT][hapmap]
rs711027	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs711032	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs711033	0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs711041	0.83[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs711048	0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs711052	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs711054	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs711059	0.94[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs711060	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7820792	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7822198	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7822220	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7829180	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs783507	0.82[GIH][hapmap];0.85[JPT][hapmap]
rs783508	0.85[JPT][hapmap]
rs783509	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs783788	0.85[JPT][hapmap]
rs783789	0.85[JPT][hapmap]
rs783791	0.85[JPT][hapmap]
rs7845599	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs9298424	0.96[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831375	chr8:85272352-85463621	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv3481417	chr8:85279453-86145229	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv3481418	chr8:85279453-86145229	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1947960	PSKH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:85460600-85461600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:85461200-85461800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:85461200-85461800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr8:85461200-85461800	Enhancers	Right Atrium	heart
5	chr8:85461200-85462200	Enhancers	HUES6 Cell Line	embryonic stem cell

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