Variant report

Variant	rs4658040
Chromosome Location	chr1:196538912-196538913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10737676	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs10737678	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs10754192	0.89[ASW][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs10754193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754194	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs10754197	0.86[AFR][1000 genomes]
rs10922064	0.90[GIH][hapmap]
rs10922065	0.90[GIH][hapmap]
rs10922087	0.95[AFR][1000 genomes]
rs12072649	0.88[ASW][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs12075206	0.90[GIH][hapmap]
rs12117379	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12128544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130004	1.00[ASN][1000 genomes]
rs12133309	1.00[ASN][1000 genomes]
rs12133639	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133987	0.87[AFR][1000 genomes]
rs12136798	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144706	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239898	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13375567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360143	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs1416960	0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs1538683	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1571489	0.91[YRI][hapmap];0.97[AFR][1000 genomes]
rs2183225	1.00[CEU][hapmap]
rs2335906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28620995	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294368	1.00[ASW][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs4314834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405100	0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs4507960	1.00[CEU][hapmap]
rs4515738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4518841	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs4562566	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs4601531	0.87[YRI][hapmap];0.97[AFR][1000 genomes]
rs4614205	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs4625226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4633231	0.94[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs4658042	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs4658043	0.87[AFR][1000 genomes]
rs487114	1.00[CEU][hapmap]
rs499807	1.00[CEU][hapmap]
rs512900	1.00[CEU][hapmap]
rs58257510	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6688468	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6691524	0.83[ASN][1000 genomes]
rs6702610	0.84[AFR][1000 genomes]
rs73069765	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523548	1.00[ASN][1000 genomes]
rs7533533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7551203	1.00[CEU][hapmap]
rs7552170	0.84[ASW][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]

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	nsv931415	chr1:196270759-196744780	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1009233	chr1:196301712-196568874	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
3	nsv508685	chr1:196524030-196550980	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:196527800-196546200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:196527800-196559400	Weak transcription	Ovary	ovary
3	chr1:196531600-196539200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:196534200-196539000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:196534600-196541000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:196534600-196547200	Weak transcription	Liver	Liver
7	chr1:196534800-196547400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:196535800-196547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:196537200-196541000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:196537800-196541200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:196538000-196539400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:196538600-196539400	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:196538800-196539400	Enhancers	HUES48 Cell Line	embryonic stem cell

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