Variant report

Variant	rs2424955
Chromosome Location	chr20:31692076-31692077
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1007285	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11696307	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11696310	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11697605	1.00[JPT][hapmap]
rs11699009	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11699448	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700200	1.00[JPT][hapmap]
rs12625298	0.88[ASN][1000 genomes]
rs13036385	1.00[JPT][hapmap]
rs13039811	1.00[JPT][hapmap]
rs13041016	1.00[JPT][hapmap]
rs13044428	1.00[JPT][hapmap]
rs1547004	1.00[JPT][hapmap]
rs2024934	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2057261	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2057262	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070322	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070324	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2070325	0.87[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070326	1.00[JPT][hapmap]
rs2070327	0.88[ASN][1000 genomes]
rs2070328	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2073325	1.00[JPT][hapmap]
rs2424940	0.92[JPT][hapmap]
rs2424942	1.00[JPT][hapmap]
rs2424945	1.00[JPT][hapmap]
rs2424946	1.00[JPT][hapmap]
rs2424947	1.00[JPT][hapmap]
rs2424953	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424956	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424957	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424958	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424959	0.90[ASN][1000 genomes]
rs2424960	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424961	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424962	0.90[ASN][1000 genomes]
rs2424963	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424964	0.90[ASN][1000 genomes]
rs2424965	0.89[ASN][1000 genomes]
rs2889732	0.87[CHB][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34388980	0.89[ASN][1000 genomes]
rs34868076	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35268814	0.89[ASN][1000 genomes]
rs3926669	0.82[JPT][hapmap]
rs4339026	1.00[JPT][hapmap]
rs4911291	0.85[CHB][hapmap]
rs6057717	0.84[JPT][hapmap]
rs6059069	0.93[JPT][hapmap]
rs6059076	1.00[JPT][hapmap]
rs6059079	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6088091	0.80[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs6141876	0.93[JPT][hapmap]
rs6141877	0.93[JPT][hapmap]
rs7265752	1.00[JPT][hapmap]
rs7273967	0.86[ASN][1000 genomes]
rs761931	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs761933	0.84[JPT][hapmap]
rs761938	1.00[JPT][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	nsv1056411	chr20:31057037-31942835	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2758519	chr20:31495807-31748166	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758792	chr20:31495807-31748166	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2424955	TTLL9	cis	parietal	SCAN
rs2424955	C20orf71	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:31685600-31692200	Weak transcription	Right Atrium	heart
2	chr20:31688400-31693400	Weak transcription	Pancreas	Pancrea
3	chr20:31690800-31692200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr20:31691200-31699000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:31691400-31692600	Weak transcription	Adipose Nuclei	Adipose
6	chr20:31691600-31693000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:31691800-31692200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:31691800-31692600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr20:31692000-31693600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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