Variant report

Variant	rs12402879
Chromosome Location	chr1:160551013-160551014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160510071..160512136-chr1:160549726..160552800,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1055880	0.80[CEU][hapmap]
rs1061217	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10752638	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10797083	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908789	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908792	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908794	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10908796	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265443	0.83[ASN][1000 genomes]
rs11265444	0.94[ASN][1000 genomes]
rs11265449	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs11265451	0.80[ASN][1000 genomes]
rs11265452	0.84[CEU][hapmap]
rs1138323	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11583402	0.80[CEU][hapmap]
rs11585738	0.81[CEU][hapmap]
rs11590035	0.81[CEU][hapmap]
rs12048466	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs12144628	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12728784	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12736781	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1394079	0.93[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs151607	0.89[CEU][hapmap]
rs1572382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1604783	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16832283	0.84[CEU][hapmap]
rs17381453	0.81[CEU][hapmap]
rs17385407	0.81[CEU][hapmap]
rs1809963	0.81[CEU][hapmap]
rs1998651	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2025516	0.88[CEU][hapmap]
rs2025517	0.84[CEU][hapmap]
rs2083128	0.92[CEU][hapmap]
rs2089088	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2099604	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2102225	0.80[ASN][1000 genomes]
rs2102226	0.80[ASN][1000 genomes]
rs2369725	0.80[ASN][1000 genomes]
rs2369726	0.80[ASN][1000 genomes]
rs2753260	0.92[CEU][hapmap]
rs349249	0.87[ASN][1000 genomes]
rs3733264	0.81[CEU][hapmap]
rs3733265	0.81[CEU][hapmap]
rs3733266	0.81[CEU][hapmap]
rs3766387	0.84[CEU][hapmap]
rs3766388	0.85[CEU][hapmap]
rs3766389	0.81[CEU][hapmap]
rs3816146	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5002947	0.84[CEU][hapmap]
rs6427535	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6656191	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6660233	0.81[CEU][hapmap]
rs6668760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670721	0.84[CEU][hapmap]
rs6687641	0.92[CEU][hapmap]
rs6692382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521247	0.80[ASN][1000 genomes]
rs7526815	0.90[ASN][1000 genomes]
rs7528976	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7534679	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547054	0.92[CEU][hapmap]
rs7550771	0.92[CEU][hapmap]
rs927202	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs977019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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
rs12402879	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160549200-160554600	Weak transcription	Liver	Liver
2	chr1:160549400-160552000	Enhancers	Duodenum Mucosa	Duodenum
3	chr1:160549400-160552400	Enhancers	K562	blood
4	chr1:160549600-160551600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:160549600-160551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:160549600-160551600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:160549600-160552000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:160549600-160552000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr1:160549600-160552000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:160549600-160552000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:160549600-160552400	Enhancers	Fetal Intestine Small	intestine
12	chr1:160549800-160551200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr1:160549800-160551200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr1:160549800-160551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:160549800-160551800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:160549800-160551800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:160549800-160552000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:160549800-160552000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:160550000-160552000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:160550200-160552400	Enhancers	Fetal Intestine Large	intestine
21	chr1:160550400-160551600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:160550600-160552000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:160550800-160551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:160550800-160552000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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