Variant report

Variant	rs61396871
Chromosome Location	chr17:46028160-46028161
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
2	chr17:46027611..46030432-chr17:46048552..46050466,2	K562	blood:
3	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
4	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
5	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1133221	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1473117	0.86[EUR][1000 genomes]
rs16949270	0.94[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16949651	0.86[ASN][1000 genomes]
rs17616799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1962201	0.88[ASN][1000 genomes]
rs1986694	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2285860	0.91[EUR][1000 genomes]
rs2325750	0.88[ASN][1000 genomes]
rs2525105	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55956628	0.81[ASN][1000 genomes]
rs55982711	0.91[EUR][1000 genomes]
rs56006220	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56402159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57782323	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58848175	0.95[ASN][1000 genomes]
rs72823519	0.91[EUR][1000 genomes]
rs73323310	0.81[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	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	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61396871	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:89 , 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	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
5	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:46027000-46030000	Weak transcription	Psoas Muscle	Psoas
7	chr17:46027200-46028200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr17:46027200-46028200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr17:46027200-46028200	Enhancers	Fetal Thymus	thymus
10	chr17:46027200-46029200	Genic enhancers	Fetal Intestine Small	intestine
11	chr17:46027200-46030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:46027200-46031200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:46027200-46032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
15	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
16	chr17:46027400-46028200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr17:46027400-46028200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr17:46027400-46028200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:46027400-46028400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:46027400-46028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:46027400-46029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr17:46027400-46029600	Weak transcription	Lung	lung
23	chr17:46027400-46030000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr17:46027400-46030000	Genic enhancers	Stomach Mucosa	stomach
25	chr17:46027400-46030800	Strong transcription	Fetal Stomach	stomach
26	chr17:46027400-46032600	Weak transcription	NHLF	lung
27	chr17:46027400-46033800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:46027400-46033800	Weak transcription	NHDF-Ad	bronchial
29	chr17:46027400-46034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
32	chr17:46027400-46034600	Weak transcription	K562	blood
33	chr17:46027400-46034800	Weak transcription	NH-A	brain
34	chr17:46027600-46028200	Enhancers	GM12878-XiMat	blood
35	chr17:46027600-46028200	Enhancers	HMEC	breast
36	chr17:46027600-46028600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr17:46027600-46028600	Weak transcription	Gastric	stomach
38	chr17:46027600-46028600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:46027600-46028800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr17:46027600-46028800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr17:46027600-46028800	Weak transcription	Brain Anterior Caudate	brain
42	chr17:46027600-46029000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr17:46027600-46029000	Enhancers	Pancreas	Pancrea
44	chr17:46027600-46029000	Genic enhancers	Rectal Mucosa Donor 29	rectum
45	chr17:46027600-46029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr17:46027600-46029800	Genic enhancers	Rectal Mucosa Donor 31	rectum
47	chr17:46027600-46030200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:46027600-46030400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:46027600-46030400	Enhancers	Liver	Liver
50	chr17:46027600-46030400	Weak transcription	Brain Substantia Nigra	brain

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