Variant report

Variant	rs6662093
Chromosome Location	chr1:160573892-160573893
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap]
rs11265452	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs11583402	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11585738	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590035	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs12728784	0.81[CEU][hapmap]
rs1394078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151607	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs16832283	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1726	0.85[EUR][1000 genomes]
rs17381453	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17385337	0.92[CEU][hapmap]
rs17385407	1.00[CEU][hapmap]
rs17385878	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1809963	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2083128	0.84[CEU][hapmap]
rs2099604	0.82[CEU][hapmap]
rs2753260	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs3733264	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3733265	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3733266	1.00[CEU][hapmap]
rs3766385	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3766387	0.91[CEU][hapmap]
rs3766388	0.92[CEU][hapmap]
rs3766389	1.00[CEU][hapmap]
rs3816146	0.84[CEU][hapmap]
rs4145897	0.82[EUR][1000 genomes]
rs5002947	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs55841347	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56040770	0.84[EUR][1000 genomes]
rs56168064	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56367214	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61801562	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61801564	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61801565	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61801567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802605	0.82[EUR][1000 genomes]
rs61802606	0.86[EUR][1000 genomes]
rs61802608	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6687641	0.88[CEU][hapmap]
rs6692382	0.81[CEU][hapmap]
rs67197441	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72708832	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7418241	0.82[EUR][1000 genomes]
rs7547054	0.84[CEU][hapmap]
rs7550771	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs912582	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs977019	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6662093	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160555600-160575200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:160558000-160575400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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