Variant report

Variant	rs2083128
Chromosome Location	chr1:160530427-160530428
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1055880	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1061217	0.91[CEU][hapmap]
rs11265424	0.82[EUR][1000 genomes]
rs11265442	0.92[CEU][hapmap]
rs11265452	0.83[CEU][hapmap]
rs11583402	0.87[CEU][hapmap]
rs11585738	0.87[CEU][hapmap]
rs11590035	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs12144628	0.88[CEU][hapmap]
rs12402879	0.92[CEU][hapmap]
rs12728784	0.96[CEU][hapmap]
rs1394078	0.84[CEU][hapmap]
rs151607	0.88[CEU][hapmap]
rs1572382	0.92[CEU][hapmap]
rs16832283	0.83[CEU][hapmap]
rs1726	0.87[EUR][1000 genomes]
rs17381453	0.87[CEU][hapmap]
rs17385337	0.83[JPT][hapmap]
rs17385407	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs1998651	0.92[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.91[CEU][hapmap]
rs349249	0.91[EUR][1000 genomes]
rs3733264	0.87[CEU][hapmap]
rs3733265	0.87[CEU][hapmap]
rs3733266	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755898	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766384	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766385	0.84[CEU][hapmap]
rs3766387	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3766388	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766389	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816146	0.87[CEU][hapmap]
rs5002947	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs56040770	0.86[EUR][1000 genomes]
rs61802608	0.81[EUR][1000 genomes]
rs6668760	0.92[CEU][hapmap]
rs6670721	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs6687641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692382	0.92[CEU][hapmap]
rs67197441	0.81[EUR][1000 genomes]
rs72708832	0.81[EUR][1000 genomes]
rs7547054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550771	0.91[CEU][hapmap]
rs912582	0.84[CEU][hapmap]
rs977019	0.92[CEU][hapmap]

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
rs2083128	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160519800-160531000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:160523000-160543200	Weak transcription	Gastric	stomach
3	chr1:160524000-160531400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:160527800-160535200	Weak transcription	Pancreas	Pancrea
5	chr1:160528000-160531400	Enhancers	Dnd41	blood
6	chr1:160528200-160531800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:160528600-160531600	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr1:160528800-160530800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:160529000-160532000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:160529200-160530800	Weak transcription	Fetal Thymus	thymus
11	chr1:160529200-160537000	Weak transcription	K562	blood
12	chr1:160529400-160530600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr1:160529400-160535200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:160529800-160531600	Enhancers	Thymus	Thymus
15	chr1:160529800-160531800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:160530200-160530800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:160530200-160531000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:160530200-160531000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:160530200-160532200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr1:160530200-160532400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr1:160530200-160533000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:160530400-160530800	Enhancers	Primary T cells from cord blood	blood
23	chr1:160530400-160530800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:160530400-160530800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:160530400-160531000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr1:160530400-160531600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:160530400-160532400	Enhancers	Primary T helper cells fromperipheralblood	blood

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