Variant report

Variant	rs330905
Chromosome Location	chr8:8993551-8993552
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:8982946..8984687-chr8:8992540..8994989,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10089635	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12785	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs189798	0.85[EUR][1000 genomes]
rs330904	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs330908	0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs330909	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330910	0.86[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs330911	0.86[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs330912	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330913	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs330914	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs330915	0.86[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs330916	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs330917	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs330918	0.82[AMR][1000 genomes]
rs330919	0.85[CHB][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs330920	0.81[CHB][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs330921	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap]
rs330922	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs330923	0.82[CEU][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs330926	0.85[AFR][1000 genomes]
rs330927	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs408773	0.84[AMR][1000 genomes]
rs9949	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	n/a
8	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs330905	PPP1R3B	cis	lymphoblastoid	seeQTL
rs330905	FLJ10661	cis	cerebellum	SCAN
rs330905	CTSB	cis	cerebellum	SCAN
rs330905	RP1L1	cis	cerebellum	SCAN
rs330905	DEFB134	cis	cerebellum	SCAN
rs330905	DEFB136	cis	parietal	SCAN
rs330905	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8987800-8997400	Weak transcription	Spleen	Spleen
2	chr8:8989200-8997400	Weak transcription	Gastric	stomach
3	chr8:8989400-8993600	Weak transcription	K562	blood
4	chr8:8989600-8996800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr8:8990200-8995200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr8:8990400-8994800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr8:8990400-8997600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:8992000-8993600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr8:8992000-8993800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:8992200-8994200	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr8:8992200-8994200	Enhancers	NH-A	brain
12	chr8:8992200-8994400	Enhancers	Fetal Stomach	stomach
13	chr8:8992400-8993600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr8:8992400-8993600	Enhancers	Pancreas	Pancrea
15	chr8:8992400-8993800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:8992400-8993800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:8992400-8994200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr8:8992400-8994400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr8:8992400-8994400	Flanking Active TSS	NHDF-Ad	bronchial
20	chr8:8992400-8994800	Enhancers	Stomach Mucosa	stomach
21	chr8:8992600-8993600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr8:8992600-8993600	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr8:8992600-8993600	Flanking Active TSS	A549	lung
24	chr8:8992600-8993800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr8:8992600-8993800	Flanking Active TSS	HSMM	muscle
26	chr8:8992600-8994000	Enhancers	Fetal Intestine Large	intestine
27	chr8:8992600-8994200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr8:8992600-8994200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
29	chr8:8992600-8994200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr8:8992600-8994200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr8:8992600-8994200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr8:8992600-8994200	Flanking Active TSS	HSMMtube	muscle
33	chr8:8992600-8994200	Flanking Active TSS	Osteobl	bone
34	chr8:8992600-8994400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr8:8992600-8994400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr8:8992600-8994400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr8:8992600-8994400	Enhancers	Small Intestine	intestine
38	chr8:8992600-8994400	Flanking Active TSS	HUVEC	blood vessel
39	chr8:8992600-9000000	Weak transcription	Hela-S3	cervix
40	chr8:8992800-8993800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr8:8992800-8993800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr8:8992800-8994000	Active TSS	Brain Hippocampus Middle	brain
43	chr8:8992800-8994200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr8:8992800-8994400	Flanking Active TSS	Fetal Heart	heart
45	chr8:8992800-8994600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr8:8992800-8995000	Weak transcription	Lung	lung
47	chr8:8993000-8993600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr8:8993000-8993600	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr8:8993000-8993600	Flanking Active TSS	GM12878-XiMat	blood
50	chr8:8993000-8993600	Flanking Active TSS	HMEC	breast

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