Variant report

Variant	rs7528976
Chromosome Location	chr1:160499961-160499962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs1061217	0.92[ASW][hapmap];0.91[CEU][hapmap];0.92[TSI][hapmap]
rs10797073	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908789	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11265442	0.92[CEU][hapmap]
rs11265452	0.83[CEU][hapmap]
rs1138323	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11583402	0.82[CEU][hapmap]
rs11590035	0.83[CEU][hapmap]
rs12144628	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12402879	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12728784	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12736781	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs151607	0.83[CEU][hapmap]
rs1572382	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16832208	0.93[LWK][hapmap];0.93[YRI][hapmap]
rs16832283	0.83[CEU][hapmap]
rs1809963	0.83[CEU][hapmap]
rs1998651	0.92[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2025516	0.88[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2025517	0.84[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2083128	0.83[CEU][hapmap]
rs2099604	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753260	0.83[CEU][hapmap]
rs3766387	0.83[CEU][hapmap]
rs3766388	0.83[CEU][hapmap]
rs3816146	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4106115	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5002947	0.83[CEU][hapmap]
rs6656191	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660233	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6668760	0.92[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6670721	0.83[CEU][hapmap]
rs6687641	0.83[CEU][hapmap]
rs6692382	0.92[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7515302	0.93[ASN][1000 genomes]
rs7534679	0.81[EUR][1000 genomes]
rs7547054	0.83[CEU][hapmap]
rs7550771	0.83[CEU][hapmap]
rs9726326	0.90[EUR][1000 genomes]
rs977019	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.81[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
rs7528976	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160498600-160500200	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr1:160498800-160500200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr1:160498800-160500200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:160498800-160500200	Enhancers	Fetal Thymus	thymus
5	chr1:160499000-160500200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:160499000-160500200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:160499000-160500200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:160499000-160500200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:160499200-160500000	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:160499200-160500200	Enhancers	Primary T cells from cord blood	blood
11	chr1:160499200-160500200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:160499200-160500200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:160499200-160500400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:160499200-160500600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:160499600-160500200	Enhancers	Dnd41	blood
16	chr1:160499600-160500200	Enhancers	GM12878-XiMat	blood
17	chr1:160499600-160500400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:160499800-160500000	Enhancers	Primary hematopoietic stem cells	blood

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