Variant report

Variant	rs12728784
Chromosome Location	chr1:160538937-160538938
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160525622..160528580-chr1:160538384..160540586,2	K562	blood:
2	chr1:160536541..160539373-chr1:160549161..160552042,2	K562	blood:
3	chr1:160537854..160539383-chr1:160539472..160541897,2	K562	blood:
4	chr1:160533660..160535894-chr1:160538727..160540952,2	K562	blood:
5	chr1:160510384..160512674-chr1:160538457..160540708,2	K562	blood:
6	chr1:160536235..160543058-chr1:160543478..160548021,8	K562	blood:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1055880	0.83[CEU][hapmap]
rs1061217	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10752638	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10797073	0.81[AMR][1000 genomes]
rs10797083	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10908789	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10908792	0.89[EUR][1000 genomes]
rs10908794	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10908796	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11265442	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[EUR][1000 genomes]
rs11265452	0.83[CEU][hapmap]
rs1138323	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583402	0.83[CEU][hapmap]
rs11585738	0.83[CEU][hapmap]
rs11590035	0.84[CEU][hapmap]
rs12144628	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12402879	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12736781	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1394078	0.81[CEU][hapmap]
rs1394079	0.91[CHB][hapmap]
rs151607	0.88[CEU][hapmap]
rs1572382	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1604783	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16832283	0.83[CEU][hapmap]
rs17381453	0.83[CEU][hapmap]
rs17385407	0.83[CEU][hapmap]
rs1809963	0.80[CEU][hapmap]
rs1998651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2025516	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs2025517	0.84[CEU][hapmap];0.86[JPT][hapmap]
rs2083128	0.96[CEU][hapmap]
rs2099604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2753260	0.92[CEU][hapmap]
rs349249	0.91[ASN][1000 genomes]
rs3733264	0.83[CEU][hapmap]
rs3733265	0.83[CEU][hapmap]
rs3733266	0.83[CEU][hapmap]
rs3766385	0.81[CEU][hapmap]
rs3766387	0.88[CEU][hapmap]
rs3766388	0.88[CEU][hapmap]
rs3766389	0.83[CEU][hapmap]
rs3816146	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5002947	0.87[CEU][hapmap]
rs6427535	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6656191	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6660233	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6668760	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6670721	0.87[CEU][hapmap]
rs6687641	0.96[CEU][hapmap]
rs6692382	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7521247	0.98[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7528976	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534679	0.95[EUR][1000 genomes]
rs7547054	0.96[CEU][hapmap]
rs7550771	0.92[CEU][hapmap]
rs912582	0.80[CEU][hapmap]
rs977019	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[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
rs12728784	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160523000-160543200	Weak transcription	Gastric	stomach
2	chr1:160535000-160540000	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr1:160535200-160542200	Enhancers	Fetal Thymus	thymus
4	chr1:160535400-160542600	Weak transcription	Pancreas	Pancrea
5	chr1:160535400-160547600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:160536000-160547000	Weak transcription	Adipose Nuclei	Adipose
7	chr1:160536800-160539400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:160537000-160539200	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:160537200-160539000	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:160537600-160539000	Flanking Active TSS	Dnd41	blood
11	chr1:160538000-160539800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:160538000-160544200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:160538200-160539800	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:160538200-160541200	Weak transcription	Spleen	Spleen
15	chr1:160538200-160541800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:160538200-160542400	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr1:160538200-160544400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr1:160538200-160545400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:160538200-160546000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr1:160538400-160539400	Enhancers	GM12878-XiMat	blood
21	chr1:160538400-160539600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:160538400-160540800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr1:160538400-160544400	Weak transcription	K562	blood
24	chr1:160538400-160544600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:160538600-160539000	Weak transcription	Primary B cells from cord blood	blood
26	chr1:160538600-160539200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:160538600-160540200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr1:160538600-160544800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr1:160538800-160539000	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr1:160538800-160539000	Flanking Active TSS	Thymus	Thymus
31	chr1:160538800-160539200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:160538800-160540800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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