Variant report

Variant	rs56040770
Chromosome Location	chr1:160537801-160537802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160536541..160539373-chr1:160549161..160552042,2	K562	blood:
2	chr1:160521084..160523233-chr1:160536516..160538024,2	K562	blood:
3	chr1:160536235..160543058-chr1:160543478..160548021,8	K562	blood:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1055880	0.83[EUR][1000 genomes]
rs11583402	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11585738	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590035	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1394078	0.82[EUR][1000 genomes]
rs1726	0.82[EUR][1000 genomes]
rs17381453	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17385878	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2083128	0.86[EUR][1000 genomes]
rs3733264	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733265	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733266	0.82[EUR][1000 genomes]
rs3755898	0.87[EUR][1000 genomes]
rs3766384	0.87[EUR][1000 genomes]
rs3766385	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3766387	0.87[EUR][1000 genomes]
rs3766389	0.82[EUR][1000 genomes]
rs4145897	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5002947	0.82[EUR][1000 genomes]
rs61801562	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61801564	0.86[EUR][1000 genomes]
rs61801565	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61801567	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61802603	0.86[ASN][1000 genomes]
rs61802604	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802605	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61802606	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61802608	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802610	0.97[ASN][1000 genomes]
rs6662093	0.84[EUR][1000 genomes]
rs6670721	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687641	0.85[EUR][1000 genomes]
rs6697596	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6699346	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs67197441	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708818	0.86[ASN][1000 genomes]
rs72708832	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7418241	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539982	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7547054	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56040770	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160523000-160543200	Weak transcription	Gastric	stomach
2	chr1:160534600-160538200	Enhancers	Fetal Lung	lung
3	chr1:160535000-160540000	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr1:160535200-160542200	Enhancers	Fetal Thymus	thymus
5	chr1:160535400-160542600	Weak transcription	Pancreas	Pancrea
6	chr1:160535400-160547600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:160535800-160538000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:160536000-160547000	Weak transcription	Adipose Nuclei	Adipose
9	chr1:160536400-160538800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:160536800-160538200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:160536800-160538600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:160536800-160538800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160536800-160539400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:160537000-160538200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:160537000-160538200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr1:160537000-160538400	Enhancers	K562	blood
17	chr1:160537000-160539200	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:160537200-160538000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr1:160537200-160539000	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:160537400-160538000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:160537400-160538200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr1:160537400-160538400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr1:160537400-160538400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:160537600-160538000	Enhancers	Primary T cells from cord blood	blood
25	chr1:160537600-160538000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:160537600-160538200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
27	chr1:160537600-160538400	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:160537600-160538600	Enhancers	Primary B cells from cord blood	blood
29	chr1:160537600-160538600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:160537600-160539000	Flanking Active TSS	Dnd41	blood
31	chr1:160537800-160538200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
32	chr1:160537800-160538200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr1:160537800-160538200	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:160537800-160538400	Flanking Active TSS	Thymus	Thymus

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