Variant report

Variant	rs12092166
Chromosome Location	chr1:161032110-161032111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161014963..161016917-chr1:161031588..161033726,2	MCF-7	breast:
2	chr1:161030433..161032581-chr1:161036169..161038406,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11265545	0.87[AFR][1000 genomes]
rs12080904	1.00[YRI][hapmap]
rs12084390	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17175512	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs34009675	1.00[AMR][1000 genomes]
rs34618415	1.00[AMR][1000 genomes]
rs35709078	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12092166	CD84	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161016400-161037800	Weak transcription	Colonic Mucosa	Colon
2	chr1:161017000-161032200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:161017600-161034400	Strong transcription	Fetal Thymus	thymus
4	chr1:161018600-161032400	Strong transcription	Primary B cells from cord blood	blood
5	chr1:161018600-161033600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:161021400-161034000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr1:161021600-161033000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:161021600-161038400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:161024800-161038200	Weak transcription	Lung	lung
10	chr1:161026400-161039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:161026600-161036600	Weak transcription	Placenta	Placenta
12	chr1:161026800-161035000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:161027200-161036200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:161027400-161037800	Weak transcription	Esophagus	oesophagus
15	chr1:161029000-161032400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr1:161029000-161036000	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr1:161029200-161032400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:161029200-161032600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
19	chr1:161029200-161032600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:161029200-161036600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:161029400-161033000	Genic enhancers	Primary T cells from cord blood	blood
22	chr1:161029800-161036200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:161029800-161038000	Weak transcription	Stomach Mucosa	stomach
24	chr1:161030000-161033400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:161030000-161034000	Strong transcription	Primary B cells from peripheral blood	blood
26	chr1:161030000-161034000	Weak transcription	Dnd41	blood
27	chr1:161030000-161036000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:161030000-161036000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:161030000-161036800	Weak transcription	Spleen	Spleen
30	chr1:161030000-161046200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:161030800-161036200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:161031000-161034800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr1:161031600-161032400	Strong transcription	Thymus	Thymus
34	chr1:161031800-161032200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:161031800-161032200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:161031800-161032200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
37	chr1:161031800-161036400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr1:161032000-161032200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr1:161032000-161032400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:161032000-161032600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:161032000-161036400	Weak transcription	Rectal Mucosa Donor 29	rectum

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