Variant report

Variant	rs1663841
Chromosome Location	chr1:165895054-165895055
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12060526	0.89[JPT][hapmap]
rs12118019	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119028	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12569109	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768900	0.85[EUR][1000 genomes]
rs3790654	0.82[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs3790668	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790669	0.82[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs3790670	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790674	0.91[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4656464	0.85[ASN][1000 genomes]
rs4656465	0.82[ASN][1000 genomes]
rs4656467	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474766	0.92[EUR][1000 genomes]
rs475558	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504436	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505877	0.85[EUR][1000 genomes]
rs514163	0.91[CEU][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs530717	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs533929	0.92[EUR][1000 genomes]
rs537068	0.92[EUR][1000 genomes]
rs561315	0.92[EUR][1000 genomes]
rs576213	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426943	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6661905	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6682285	0.89[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6687465	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7520107	0.97[ASN][1000 genomes]
rs7547020	0.85[ASN][1000 genomes]
rs9787031	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872509	chr1:165885147-165917109	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1663841	UCK2	cis	cerebellum	SCAN
rs1663841	SLAMF1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165858600-165902400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165880800-165902600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:165883600-165896400	Weak transcription	Dnd41	blood
4	chr1:165893400-165895400	Enhancers	K562	blood
5	chr1:165894200-165895400	Enhancers	Fetal Thymus	thymus
6	chr1:165894200-165895800	Enhancers	Thymus	Thymus
7	chr1:165894400-165896800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:165894400-165902400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:165894600-165902400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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