Variant report

Variant	rs893816
Chromosome Location	chr15:74228464-74228465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74218715..74223482-chr15:74226725..74230359,5	K562	blood:
2	chr15:74226756..74229357-chr15:74247800..74251030,3	MCF-7	breast:
3	chr15:74227645..74229467-chr15:74238561..74240204,2	MCF-7	breast:
4	chr15:74227809..74230483-chr15:74244545..74246597,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129038	Chromatin interaction
ENSG00000261801	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1048661	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992314	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2028387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304722	0.82[ASW][hapmap];0.95[LWK][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs28758267	0.87[AFR][1000 genomes]
rs4077284	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886776	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58270968	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67173550	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67182653	0.86[AFR][1000 genomes]
rs893817	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893818	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893819	0.89[EUR][1000 genomes]
rs893820	1.00[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043335	chr15:74078689-74241186	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1603	chr15:74191222-74235733	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs893816	CCDC33	cis	cerebellum	SCAN
rs893816	SNX33	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74221600-74228800	Weak transcription	Aorta	Aorta
2	chr15:74221800-74231800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:74222000-74231400	Weak transcription	Left Ventricle	heart
4	chr15:74222400-74233200	Weak transcription	Fetal Thymus	thymus
5	chr15:74222600-74243200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:74223400-74230400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:74223800-74229800	Genic enhancers	Osteobl	bone
8	chr15:74224400-74231400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:74224800-74230200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:74225000-74229400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:74225200-74231400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:74225400-74229400	Enhancers	Primary hematopoietic stem cells	blood
13	chr15:74225800-74228600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:74226200-74228600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr15:74226400-74229000	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr15:74226400-74229400	Enhancers	Stomach Mucosa	stomach
17	chr15:74226400-74230000	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:74226600-74228600	Enhancers	Right Atrium	heart
19	chr15:74226600-74229200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr15:74226600-74229600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:74226800-74229400	Enhancers	NHEK	skin
22	chr15:74226800-74229800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:74227000-74228600	Enhancers	HSMM	muscle
24	chr15:74227000-74229200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:74227200-74229200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:74227200-74229400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:74227200-74229600	Enhancers	Duodenum Mucosa	Duodenum
28	chr15:74227200-74230000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:74227200-74230000	Enhancers	Placenta	Placenta
30	chr15:74227200-74230000	Genic enhancers	Fetal Stomach	stomach
31	chr15:74227400-74229200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:74227400-74229200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr15:74227400-74229400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:74227400-74229400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:74227400-74229400	Enhancers	Fetal Muscle Trunk	muscle
36	chr15:74227400-74229600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr15:74227400-74229600	Enhancers	Fetal Lung	lung
38	chr15:74227400-74229600	Enhancers	HMEC	breast
39	chr15:74227400-74230000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:74227600-74229000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:74227600-74229000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:74227600-74229200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr15:74227600-74231200	Weak transcription	HSMMtube	muscle
44	chr15:74227600-74231200	Weak transcription	NHDF-Ad	bronchial
45	chr15:74227600-74233000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:74227600-74236600	Weak transcription	Thymus	Thymus
47	chr15:74227800-74228800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:74227800-74229000	Enhancers	Colon Smooth Muscle	Colon
49	chr15:74227800-74230000	Enhancers	Spleen	Spleen
50	chr15:74227800-74233800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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