Variant report

Variant	rs7558803
Chromosome Location	chr2:142820874-142820875
allele	A/C
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:77)

rs_ID	r²[population]
rs1001629	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10803487	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs10928133	0.94[ASN][1000 genomes]
rs10928134	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11677754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680286	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap]
rs11688838	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691560	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs11691595	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs11692364	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12105566	0.98[ASN][1000 genomes]
rs12105584	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12470890	0.81[CHB][hapmap]
rs12618881	0.98[ASN][1000 genomes]
rs12619411	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs12621782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998297	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13000270	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13036224	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1349219	0.81[CHB][hapmap]
rs1349221	0.81[CHB][hapmap]
rs1349222	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1375603	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1375609	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs1375613	0.93[GIH][hapmap];0.95[TSI][hapmap]
rs1375616	0.91[ASN][1000 genomes]
rs1449475	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1449476	0.80[CHB][hapmap]
rs1449477	0.80[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap]
rs1449478	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs1449480	0.82[CHD][hapmap]
rs1449481	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1449482	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs1449485	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1449489	0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1449490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1449494	0.91[ASN][1000 genomes]
rs1449495	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1449496	0.91[ASN][1000 genomes]
rs1449498	0.95[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449499	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1449501	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1449503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1449504	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17824487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868542	0.81[CHB][hapmap]
rs1868543	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1868544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1900933	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1900934	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2029142	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2060592	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2167053	0.81[CHB][hapmap]
rs2197910	1.00[ASN][1000 genomes]
rs2218734	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2381203	0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs34392492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662219	0.82[CHD][hapmap];0.86[MEX][hapmap];0.80[ASN][1000 genomes]
rs4662370	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4662373	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62155598	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62157626	0.91[ASN][1000 genomes]
rs62157627	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744928	0.81[CHB][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs6754907	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566250	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs7581031	0.81[CHB][hapmap]
rs7586417	0.80[ASN][1000 genomes]
rs7598886	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][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]
rs7605112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608258	0.81[CHB][hapmap]
rs7609479	0.82[CHD][hapmap]
rs957376	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap]
rs993935	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9941495	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941695	0.98[ASN][1000 genomes]
rs997123	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530398	chr2:142474842-142843839	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875253	chr2:142805006-142855291	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7558803	HNMT	cis	parietal	SCAN
rs7558803	NXPH2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142811600-142821400	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:142818400-142821400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:142819800-142821400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:142820000-142821800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:142820200-142821400	Weak transcription	Brain Substantia Nigra	brain

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