Variant report

Variant	rs475032
Chromosome Location	chr11:64140737-64140738
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64130858..64133466-chr11:64138873..64141793,3	K562	blood:
2	chr11:64140396..64140949-chr5:180454894..180455621,2	HCT-116	colon:
3	chr11:64122785..64130803-chr11:64136171..64143726,15	K562	blood:
4	chr11:64138832..64141064-chr11:64144568..64147426,2	K562	blood:
5	chr11:64129822..64132037-chr11:64139114..64141435,2	MCF-7	breast:
6	chr11:64140417..64141121-chr16:3073843..3074445,2	HCT-116	colon:
7	chr11:64140352..64141276-chr8:103667092..103668087,2	Hela-S3	cervix:
8	chr11:64140082..64140827-chr17:72634912..72635414,2	HCT-116	colon:
9	chr11:64121829..64128526-chr11:64138236..64143726,11	K562	blood:
10	chr11:64135284..64138280-chr11:64138462..64142226,6	K562	blood:
11	chr11:64139080..64141620-chr11:64144256..64148089,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction
ENSG00000221273	Chromatin interaction
ENSG00000168071	Chromatin interaction
ENSG00000162302	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10897487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231770	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231771	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231772	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542299	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601651	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606015	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1198984	0.81[AFR][1000 genomes]
rs1199045	0.85[EUR][1000 genomes]
rs1199046	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199047	0.85[EUR][1000 genomes]
rs1662188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17857342	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474901	0.81[ASN][1000 genomes]
rs508168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510372	0.82[EUR][1000 genomes]
rs516124	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519763	0.80[ASN][1000 genomes]
rs521950	0.97[ASN][1000 genomes]
rs527465	0.96[ASN][1000 genomes]
rs538147	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566128	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs600377	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs612448	0.80[ASN][1000 genomes]
rs61886926	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs641168	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs645078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72926005	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72926006	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs475032	CCDC88	cis	multi-tissue	Pritchard
rs475032	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs475032	CCDC88B	cis	Cerebellum	GTEx
rs475032	CCDC88B	cis	multi-tissue	Pritchard
rs475032	AP003774.1	cis	Whole Blood	GTEx
rs475032	CCDC88B	cis	Lymphoblastoid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64127400-64144400	Weak transcription	Psoas Muscle	Psoas
2	chr11:64127800-64146800	Weak transcription	Fetal Heart	heart
3	chr11:64130000-64142400	Weak transcription	Stomach Mucosa	stomach
4	chr11:64134400-64140800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:64134400-64150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:64134400-64158400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:64134600-64140800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr11:64134600-64140800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:64135600-64143000	Weak transcription	NH-A	brain
10	chr11:64135600-64145800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:64135600-64148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:64136000-64145800	Weak transcription	HSMMtube	muscle
13	chr11:64138000-64140800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:64138000-64140800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:64138000-64141000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:64138000-64141200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:64138000-64142800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:64138000-64145800	Weak transcription	Osteobl	bone
19	chr11:64138000-64146000	Weak transcription	HMEC	breast
20	chr11:64138200-64141200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr11:64138200-64142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:64138200-64146000	Weak transcription	Pancreas	Pancrea
23	chr11:64138200-64147200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:64138200-64151600	Weak transcription	Left Ventricle	heart
25	chr11:64138400-64142400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:64138400-64143800	Weak transcription	NHLF	lung
27	chr11:64138400-64144000	Weak transcription	Aorta	Aorta
28	chr11:64138600-64141200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:64138800-64146200	Weak transcription	Esophagus	oesophagus
30	chr11:64139000-64140800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:64139000-64146000	Weak transcription	Right Ventricle	heart
32	chr11:64139200-64140800	Weak transcription	Primary B cells from cord blood	blood
33	chr11:64139200-64141000	Weak transcription	Fetal Muscle Leg	muscle
34	chr11:64139200-64141200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:64139200-64143000	Weak transcription	Small Intestine	intestine
36	chr11:64139400-64140800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr11:64139400-64141200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr11:64139400-64141400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:64139400-64141400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:64139600-64140800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:64139600-64140800	Weak transcription	Fetal Thymus	thymus
42	chr11:64139600-64142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr11:64139600-64145800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:64139600-64146200	Weak transcription	Gastric	stomach
45	chr11:64139600-64147400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:64139600-64148000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:64139800-64140800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:64139800-64140800	Weak transcription	Fetal Intestine Small	intestine
49	chr11:64139800-64141200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:64139800-64145000	Weak transcription	Primary T cells from cord blood	blood

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