Variant report

Variant	rs17163742
Chromosome Location	chr1:223329283-223329284
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223314512..223320175-chr1:223328849..223336149,9	MCF-7	breast:
2	chr1:223318487..223320795-chr1:223328403..223334378,5	K562	blood:

Variant related genes	Relation type
ENSG00000236846	Chromatin interaction
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10489492	0.96[EUR][1000 genomes]
rs11486079	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11488549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1341985	1.00[CHB][hapmap]
rs1361642	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1418145	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1418146	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1612398	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1640809	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1640811	1.00[CEU][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1640812	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1640813	1.00[CEU][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1640814	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1640815	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1640817	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1640818	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1640819	0.80[AMR][1000 genomes]
rs1640823	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17163741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17163743	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1773738	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1773744	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1773749	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1773754	1.00[EUR][1000 genomes]
rs1773761	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1773762	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1773763	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1773765	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1773766	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1773767	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1773768	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1935305	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2256707	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2353474	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2430400	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2487834	0.93[EUR][1000 genomes]
rs2487836	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34136554	0.89[EUR][1000 genomes]
rs34552707	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34970812	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35349967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35579200	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35705006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35802580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35953839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4393150	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5744106	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs5744107	1.00[CHB][hapmap];1.00[GIH][hapmap]
rs66553000	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs66662427	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66757010	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66832195	0.89[EUR][1000 genomes]
rs66938974	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67573944	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67623966	1.00[EUR][1000 genomes]
rs67639934	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67833495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67883821	1.00[EUR][1000 genomes]
rs723961	0.89[EUR][1000 genomes]
rs72743851	0.96[EUR][1000 genomes]
rs72743852	0.96[EUR][1000 genomes]
rs73118159	1.00[EUR][1000 genomes]
rs759303	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs763389	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs988241	1.00[CEU][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs988242	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs988243	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs988244	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223327200-223334600	Weak transcription	Fetal Thymus	thymus
2	chr1:223328600-223329800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:223329000-223331000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:223329200-223338600	Weak transcription	Placenta	Placenta

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