Variant report

Variant	rs56402159
Chromosome Location	chr17:46031322-46031323
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45971561..45975471-chr17:46029521..46031921,4	MCF-7	breast:
2	chr17:45928850..45930934-chr17:46029439..46031345,2	K562	blood:
3	chr17:45962826..45965067-chr17:46029549..46031610,2	MCF-7	breast:
4	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
5	chr17:46029177..46031751-chr17:46099712..46102366,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1133221	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1473117	0.86[EUR][1000 genomes]
rs16949270	0.94[AFR][1000 genomes]
rs16949651	0.85[ASN][1000 genomes]
rs17616799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962201	0.87[ASN][1000 genomes]
rs1986694	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2285860	0.91[EUR][1000 genomes]
rs2325750	0.86[ASN][1000 genomes]
rs2525105	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55982711	0.91[EUR][1000 genomes]
rs56006220	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs57782323	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58848175	0.97[ASN][1000 genomes]
rs61396871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72823519	0.91[EUR][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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56402159	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr17:46027200-46032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
7	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
8	chr17:46027400-46032600	Weak transcription	NHLF	lung
9	chr17:46027400-46033800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr17:46027400-46033800	Weak transcription	NHDF-Ad	bronchial
11	chr17:46027400-46034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
14	chr17:46027400-46034600	Weak transcription	K562	blood
15	chr17:46027400-46034800	Weak transcription	NH-A	brain
16	chr17:46027600-46031600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr17:46027600-46032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:46027600-46032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:46027600-46033000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:46027600-46033800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr17:46027600-46034200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:46027600-46034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:46027600-46034800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
25	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr17:46027800-46031600	Weak transcription	Small Intestine	intestine
27	chr17:46027800-46032200	Weak transcription	Primary B cells from cord blood	blood
28	chr17:46027800-46032600	Weak transcription	A549	lung
29	chr17:46027800-46032800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:46027800-46033600	Weak transcription	Brain Angular Gyrus	brain
31	chr17:46027800-46034000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr17:46027800-46034200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr17:46028000-46032800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr17:46028000-46033000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr17:46028200-46031400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr17:46028200-46032800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:46028200-46032800	Weak transcription	HMEC	breast
40	chr17:46029000-46032200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
41	chr17:46029200-46031400	Strong transcription	NHEK	skin
42	chr17:46029200-46035200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
43	chr17:46029400-46032600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:46029600-46031400	Strong transcription	Primary T cells from cord blood	blood
45	chr17:46029600-46031400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr17:46029600-46031800	Genic enhancers	Lung	lung
47	chr17:46029600-46032200	Transcr. at gene 5' and 3'	Pancreas	Pancrea
48	chr17:46029600-46034600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:46029800-46032600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr17:46029800-46034200	Weak transcription	Brain Anterior Caudate	brain

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