Variant report

Variant	rs1990057
Chromosome Location	chr7:147735399-147735400
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:147734255..147736925-chr7:147737815..147740650,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10250079	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10253458	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10264877	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10272032	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10279570	0.85[CEU][hapmap]
rs10280388	0.91[CEU][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10281082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10485848	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10500195	0.90[CEU][hapmap]
rs10952721	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10952722	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10952723	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10952724	0.90[CEU][hapmap]
rs10952725	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10952726	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10952727	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11764815	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12055952	0.95[CEU][hapmap]
rs12531913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532338	0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[MEX][hapmap]
rs12532341	0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[MEX][hapmap]
rs12539260	0.95[CEU][hapmap]
rs12667149	1.00[CEU][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12671605	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12673714	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12674206	0.90[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12674208	0.95[CEU][hapmap]
rs12703988	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12703990	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12703991	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12703992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16882145	0.95[CEU][hapmap];0.80[GIH][hapmap]
rs16883782	0.95[CEU][hapmap]
rs17133865	0.95[CEU][hapmap]
rs17170796	0.95[CEU][hapmap]
rs17546472	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1990058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2214680	0.94[CHB][hapmap]
rs2373289	1.00[CEU][hapmap]
rs2373314	0.94[CHB][hapmap]
rs2373316	0.94[CHB][hapmap]
rs2527047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2527054	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2527055	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2527058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2527059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2527060	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2527063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2527064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2527065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2527066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs2707558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707561	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707565	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707582	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2707583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2710137	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2710143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs2710152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2888540	0.88[MEX][hapmap]
rs2888547	0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[MEX][hapmap]
rs4262258	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4296960	0.88[MEX][hapmap]
rs4571660	0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4725761	0.95[CEU][hapmap];0.83[GIH][hapmap]
rs4726900	0.84[MEX][hapmap]
rs4726904	1.00[CEU][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4726905	1.00[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4726906	1.00[CEU][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4726907	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4726913	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4726914	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4726915	0.90[CEU][hapmap]
rs4726916	0.86[ASN][1000 genomes]
rs6960266	1.00[CEU][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6965599	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6979577	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs715183	0.95[CEU][hapmap]
rs757695	0.95[CEU][hapmap]
rs757697	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7797264	0.94[CHB][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9640249	0.95[CEU][hapmap]
rs9640250	0.90[CEU][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	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	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
rs1990057	ACCN3	cis	cerebellum	SCAN
rs1990057	EZH2	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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