Variant report

Variant	rs2990996
Chromosome Location	chr1:190145227-190145228
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10920691	0.81[TSI][hapmap]
rs12022837	0.81[TSI][hapmap]
rs12118393	0.81[TSI][hapmap]
rs1342913	0.83[MEX][hapmap]
rs1412966	0.82[JPT][hapmap]
rs1412970	0.83[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1418803	0.87[MEX][hapmap]
rs1592250	0.94[AFR][1000 genomes]
rs1726565	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs17481	0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs1819497	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1831781	0.82[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs1935874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247188	0.83[AMR][1000 genomes]
rs2247204	0.80[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs2249762	0.85[AMR][1000 genomes]
rs2253618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488477	0.85[AMR][1000 genomes]
rs504631	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs505600	0.80[MEX][hapmap]
rs652953	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs7511657	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs7542545	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs815332	0.86[AMR][1000 genomes]
rs815333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs815344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs815346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs815348	0.81[JPT][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548532	chr1:189758772-190371671	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917005	chr1:189855484-190259380	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv832104	chr1:189990148-190186708	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1003035	chr1:190123195-190291554	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv872755	chr1:190135811-190186387	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190140400-190148800	Weak transcription	NH-A	brain
2	chr1:190140400-190149000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:190142800-190146000	Weak transcription	HSMM	muscle
4	chr1:190143800-190146200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:190145000-190145800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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