Variant report

Variant	rs13101685
Chromosome Location	chr4:55853268-55853269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1075065	0.99[ASN][1000 genomes]
rs11941928	0.91[ASN][1000 genomes]
rs12502309	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640896	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101326	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13101777	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13104623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13106311	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13110915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111813	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13111838	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13114647	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125964	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126236	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13127180	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13127753	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13129153	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13130324	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13138898	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13144612	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146834	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4259115	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4317261	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4320192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4334808	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4336286	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4337782	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4356964	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4524450	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4569809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4599477	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57266861	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61696777	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554219	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6554222	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554223	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6820549	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6821744	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822352	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6824426	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6826834	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71624987	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7657044	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7667898	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv948758	chr4:55748430-55887962	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829938	chr4:55836964-55857893	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13101685	RPL21P44	cis	parietal	SCAN
rs13101685	SCFD2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55851400-55853400	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:55851400-55853400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr4:55851800-55853600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr4:55852000-55853600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:55852200-55853400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr4:55852200-55853400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr4:55852600-55853400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:55853000-55853400	Enhancers	HUES6 Cell Line	embryonic stem cell

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