Variant report

Variant	rs61801564
Chromosome Location	chr1:160553944-160553945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1055880	0.80[EUR][1000 genomes]
rs11583402	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11585738	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11590035	0.86[EUR][1000 genomes]
rs1394078	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16832283	0.80[EUR][1000 genomes]
rs1726	0.81[EUR][1000 genomes]
rs17381453	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17385878	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1809963	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3733264	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3733265	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3766385	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4145897	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs5002947	0.81[EUR][1000 genomes]
rs55841347	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56040770	0.86[EUR][1000 genomes]
rs56168064	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56367214	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61801562	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61801565	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61801567	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802604	0.82[AMR][1000 genomes]
rs61802605	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61802606	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61802608	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6662093	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6670721	0.86[EUR][1000 genomes]
rs6697596	0.82[AMR][1000 genomes]
rs6699346	0.82[AMR][1000 genomes]
rs67197441	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72708832	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7418241	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539982	0.82[AMR][1000 genomes]
rs7550771	0.81[AMR][1000 genomes]
rs912582	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]

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
rs61801564	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160549200-160554600	Weak transcription	Liver	Liver
2	chr1:160551200-160558400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:160551600-160557400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:160551600-160558600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:160552000-160554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:160552000-160554400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:160552000-160554400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:160552000-160554400	Weak transcription	HepG2	liver
9	chr1:160552000-160554600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:160552000-160554600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:160552000-160554600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:160552000-160554800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:160552000-160554800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:160552000-160555000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:160552600-160554600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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