Variant report

Variant	rs11542299
Chromosome Location	chr11:64138805-64138806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64126994..64130294-chr11:64137012..64139109,4	MCF-7	breast:
2	chr11:64073546..64075499-chr11:64138641..64140320,2	K562	blood:
3	chr11:64122785..64130803-chr11:64136171..64143726,15	K562	blood:
4	chr11:64136140..64139047-chr11:64144668..64147875,3	MCF-7	breast:
5	chr11:64121829..64128526-chr11:64138236..64143726,11	K562	blood:
6	chr11:64135284..64138280-chr11:64138462..64142226,6	K562	blood:

Variant related genes	Relation type
ENSG00000162302	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000173153	Chromatin interaction
ENSG00000221273	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10897487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10897488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601651	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601860	0.82[AMR][1000 genomes]
rs11606015	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11606081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1199045	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199046	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199047	0.85[EUR][1000 genomes]
rs1662188	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17857342	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3132740	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474901	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs475032	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs510372	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs516124	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519763	0.80[AMR][1000 genomes]
rs521950	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs527465	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs538147	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs542907	0.80[AMR][1000 genomes]
rs566128	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs574835	0.83[AMR][1000 genomes]
rs600377	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61886926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs645078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72926005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72926006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11542299	CCDC88B	cis	multi-tissue	Pritchard
rs11542299	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs11542299	AP003774.1	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64127400-64140000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:64127400-64144400	Weak transcription	Psoas Muscle	Psoas
3	chr11:64127600-64139600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:64127800-64139800	Strong transcription	Fetal Intestine Small	intestine
5	chr11:64127800-64146800	Weak transcription	Fetal Heart	heart
6	chr11:64128000-64139000	Strong transcription	Primary T cells from cord blood	blood
7	chr11:64128000-64139000	Strong transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:64128000-64140000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:64128200-64139400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:64128200-64139600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr11:64128200-64139600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:64128200-64139800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:64128200-64140000	Strong transcription	Lung	lung
14	chr11:64128400-64139000	Strong transcription	Adipose Nuclei	Adipose
15	chr11:64128400-64139400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:64128400-64139600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:64128400-64140400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:64128600-64139200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr11:64128800-64139800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:64129000-64139600	Strong transcription	Gastric	stomach
21	chr11:64129000-64140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:64129200-64139800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr11:64129400-64140200	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr11:64130000-64140000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:64130000-64142400	Weak transcription	Stomach Mucosa	stomach
26	chr11:64130200-64140000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr11:64131000-64140600	Weak transcription	HepG2	liver
28	chr11:64132800-64139200	Strong transcription	Small Intestine	intestine
29	chr11:64132800-64140400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr11:64133000-64139200	Strong transcription	Fetal Muscle Leg	muscle
31	chr11:64133200-64139600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:64133200-64140400	Weak transcription	HUVEC	blood vessel
33	chr11:64134000-64139000	Strong transcription	Right Ventricle	heart
34	chr11:64134400-64139800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:64134400-64140200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr11:64134400-64140600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:64134400-64140800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:64134400-64150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr11:64134400-64158400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:64134600-64140800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr11:64134600-64140800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:64134800-64140400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:64135400-64140000	Weak transcription	Brain Angular Gyrus	brain
44	chr11:64135400-64140000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr11:64135400-64140000	Weak transcription	K562	blood
46	chr11:64135400-64140600	Weak transcription	HSMM	muscle
47	chr11:64135600-64143000	Weak transcription	NH-A	brain
48	chr11:64135600-64145800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:64135600-64148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr11:64135800-64139000	Strong transcription	Placenta	Placenta

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