Variant report

Variant	rs646153
Chromosome Location	chr11:64089588-64089589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64089583-64091382	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64088399..64090085-chr11:64108067..64109781,2	K562	blood:
2	chr11:64080424..64082742-chr11:64087836..64089849,2	MCF-7	breast:
3	chr11:64088256..64090312-chr11:64092623..64094945,2	MCF-7	breast:
4	chr11:64087466..64090452-chr11:64106941..64109054,2	MCF-7	breast:
5	chr11:64059173..64060678-chr11:64089016..64091569,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRMT112	TF binding region
ENSG00000173153	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000182450	Chromatin interaction
ENSG00000257069	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11231757	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601860	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1199045	0.81[AMR][1000 genomes]
rs1199046	0.85[AMR][1000 genomes]
rs1783521	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2510066	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs474901	0.80[AFR][1000 genomes]
rs479552	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs479777	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs499425	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs510372	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs516124	0.83[AMR][1000 genomes]
rs519763	0.80[AFR][1000 genomes]
rs538147	0.81[AMR][1000 genomes]
rs542907	0.80[AFR][1000 genomes]
rs566128	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs574087	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs574835	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs612448	0.80[AFR][1000 genomes]
rs61886886	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627425	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647152	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs663743	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs694739	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs887314	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
2	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
3	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
5	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
6	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
7	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
8	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer 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 miRNA target site	237 gene(s)	inside rSNPs	diseases
9	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
10	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
11	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
12	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
13	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
14	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
15	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
16	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
17	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
18	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
19	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
20	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
21	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs646153	CCDC88B	cis	Esophagus Mucosa	GTEx
rs646153	AP003774.1	cis	Whole Blood	GTEx
rs646153	CCDC88B	cis	multi-tissue	Pritchard
rs646153	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs646153	CCDC88B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64086200-64090200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64086800-64096600	Weak transcription	Right Atrium	heart
3	chr11:64086800-64099000	Weak transcription	Small Intestine	intestine
4	chr11:64087000-64089800	Enhancers	Stomach Mucosa	stomach
5	chr11:64087000-64091000	Genic enhancers	Fetal Intestine Small	intestine
6	chr11:64087000-64091400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:64087000-64091600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:64087000-64097200	Weak transcription	HSMMtube	muscle
9	chr11:64087000-64099000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:64087000-64099000	Weak transcription	HSMM	muscle
11	chr11:64087000-64108200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:64087200-64089800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:64087200-64089800	Weak transcription	Ovary	ovary
14	chr11:64087200-64090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:64087200-64090400	Weak transcription	Primary B cells from cord blood	blood
16	chr11:64087200-64091400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr11:64087200-64091400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr11:64087200-64091600	Strong transcription	Fetal Muscle Leg	muscle
19	chr11:64087200-64091600	Strong transcription	Fetal Stomach	stomach
20	chr11:64087200-64098800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr11:64087200-64099000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:64087200-64099000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:64087400-64089600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr11:64087400-64089600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:64087400-64089600	Weak transcription	Brain Angular Gyrus	brain
26	chr11:64087400-64089800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:64087400-64090000	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:64087400-64090000	Weak transcription	Fetal Brain Male	brain
29	chr11:64087400-64090200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:64087400-64090200	Strong transcription	Spleen	Spleen
31	chr11:64087400-64090400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:64087400-64090600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr11:64087400-64091000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr11:64087400-64091000	Genic enhancers	HMEC	breast
35	chr11:64087400-64091200	Strong transcription	Adipose Nuclei	Adipose
36	chr11:64087400-64091600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:64087400-64093200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr11:64087400-64096800	Weak transcription	Psoas Muscle	Psoas
39	chr11:64087400-64097000	Weak transcription	HUVEC	blood vessel
40	chr11:64087400-64099000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:64087400-64099000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:64087600-64089800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:64087600-64089800	Weak transcription	K562	blood
44	chr11:64087600-64090000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:64087600-64090600	Strong transcription	Left Ventricle	heart
46	chr11:64087600-64091600	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr11:64087800-64089600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:64087800-64089800	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr11:64087800-64090600	Strong transcription	Brain Hippocampus Middle	brain
50	chr11:64087800-64090800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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