Variant report

Variant	rs10759631
Chromosome Location	chr9:115996044-115996045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115995999..115998465-chr9:116001136..116003648,2	K562	blood:
2	chr9:115990891..115993253-chr9:115993931..115999009,4	K562	blood:
3	chr9:115991545..115993932-chr9:115995693..115997298,2	K562	blood:
4	chr9:115995531..115997450-chr9:115998162..116001080,2	MCF-7	breast:
5	chr9:115983851..115985489-chr9:115994207..115996988,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136868	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10081797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10114381	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114423	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10121845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739389	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739391	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759635	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817460	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10817465	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10817467	0.84[AMR][1000 genomes]
rs10817470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338803	0.82[AMR][1000 genomes]
rs3810914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851623	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs7855694	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859189	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised 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	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10759631	PRPF4	cis	Thyroid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115985000-115996200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
3	chr9:115985200-115998000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:115985200-116001800	Weak transcription	Pancreas	Pancrea
5	chr9:115985600-115997600	Weak transcription	Brain Germinal Matrix	brain
6	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr9:115985800-116018400	Weak transcription	NHEK	skin
8	chr9:115985800-116019000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:115985800-116021000	Weak transcription	Fetal Stomach	stomach
10	chr9:115986400-116013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:115987600-115998600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:115987600-116017800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:115987600-116018200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:115987800-116011000	Weak transcription	A549	lung
15	chr9:115987800-116021000	Weak transcription	Hela-S3	cervix
16	chr9:115989000-116019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:115989200-116005600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:115990800-115996200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:115991000-116011600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:115992800-115996200	Weak transcription	Lung	lung
21	chr9:115994600-115996200	Enhancers	Primary hematopoietic stem cells	blood
22	chr9:115994600-115996400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr9:115994600-115996400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr9:115994800-115996200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:115994800-115996200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:115995000-115996200	Flanking Active TSS	GM12878-XiMat	blood
27	chr9:115995000-115996200	Enhancers	NHLF	lung
28	chr9:115995200-115996200	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr9:115995200-115996200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:115995200-115996200	Enhancers	Fetal Lung	lung
31	chr9:115995200-115996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr9:115995200-115996400	Enhancers	Adipose Nuclei	Adipose
33	chr9:115995200-115996600	Enhancers	Stomach Mucosa	stomach
34	chr9:115995200-116017800	Weak transcription	Left Ventricle	heart
35	chr9:115995400-115996200	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr9:115995400-115996400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:115995400-115996400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:115995400-115996600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:115995400-116009200	Weak transcription	K562	blood
40	chr9:115995400-116018000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:115995600-115996200	Enhancers	Primary B cells from cord blood	blood
42	chr9:115995600-115996400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr9:115995800-115996200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:115995800-115996200	Enhancers	Primary T cells from cord blood	blood
45	chr9:115995800-115996200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:115995800-115996400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:115995800-115997800	Weak transcription	Small Intestine	intestine
48	chr9:115995800-115998600	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr9:115995800-115999400	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr9:115995800-116005200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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