Variant report

Variant	rs9870661
Chromosome Location	chr3:143571267-143571268
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10433436	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11714060	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319100	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1319101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1394398	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1394402	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1979911	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995529	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1995530	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2011290	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361202	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2361203	0.94[EUR][1000 genomes]
rs2361205	0.94[EUR][1000 genomes]
rs2361206	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361207	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2361208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2361209	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2885193	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885194	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2885195	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4286430	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4499594	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839612	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839671	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839672	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4839673	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4839674	1.00[CEU][hapmap]
rs6440195	1.00[CEU][hapmap]
rs6440196	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6768702	1.00[EUR][1000 genomes]
rs6780027	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6782974	1.00[CEU][hapmap]
rs7623477	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7627020	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629598	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645681	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9289669	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9824974	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9836851	0.84[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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9870661	C14orf143	trans	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143569200-143573000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:143569200-143573800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:143569400-143573200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr3:143569600-143572600	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143569600-143572800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:143569600-143573200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr3:143569600-143574000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:143569600-143574000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:143569600-143574000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:143569800-143572400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:143570000-143572800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:143570000-143573000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr3:143570600-143573400	Weak transcription	Fetal Thymus	thymus
14	chr3:143571000-143574000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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