Variant report

Variant	rs8417
Chromosome Location	chr8:11667179-11667180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11658127..11661675-chr8:11664375..11667732,3	K562	blood:
2	chr8:11666673..11669607-chr8:11678720..11681322,2	K562	blood:
3	chr8:11665243..11667469-chr8:11710761..11712863,3	MCF-7	breast:
4	chr8:11625432..11628777-chr8:11664764..11667821,4	MCF-7	breast:
5	chr8:11663695..11667740-chr8:11686501..11689379,3	MCF-7	breast:
6	chr8:11658229..11662389-chr8:11662980..11669380,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154328	Chromatin interaction
ENSG00000079459	Chromatin interaction
ENSG00000255046	Chromatin interaction
ENSG00000164733	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1534863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1736058	1.00[ASW][hapmap];0.85[CHB][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1736093	0.85[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1736108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1736115	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised 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	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv890363	chr8:11647941-11681825	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv890364	chr8:11654796-11671041	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
18	nsv890365	chr8:11666451-11735641	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv890366	chr8:11666451-11900847	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
20	nsv1031158	chr8:11666558-11759064	Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv539477	chr8:11666558-11759064	Enhancers Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8417	CTSB	cis	parietal	SCAN
rs8417	CTSB	cis	lymphoblastoid	seeQTL
rs8417	CTSB	cis	cerebellum	SCAN
rs8417	NEIL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11660400-11668200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr8:11661000-11667200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:11664200-11669000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:11665000-11667200	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr8:11665200-11667200	Active TSS	Ovary	ovary
6	chr8:11665400-11667200	Active TSS	Brain Anterior Caudate	brain
7	chr8:11665400-11667200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:11665600-11667200	Active TSS	Brain Cingulate Gyrus	brain
9	chr8:11665600-11667200	Active TSS	Brain Substantia Nigra	brain
10	chr8:11665600-11667200	Active TSS	Colon Smooth Muscle	Colon
11	chr8:11665600-11667200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr8:11665600-11667200	Active TSS	Left Ventricle	heart
13	chr8:11665600-11667200	Active TSS	Right Ventricle	heart
14	chr8:11665800-11667200	Active TSS	Brain Angular Gyrus	brain
15	chr8:11665800-11667200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr8:11666200-11667200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr8:11666200-11667200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:11666200-11667200	Flanking Active TSS	Liver	Liver
19	chr8:11666200-11667200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr8:11666200-11668000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr8:11666400-11667200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:11666400-11667200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr8:11666400-11667200	Active TSS	Right Atrium	heart
24	chr8:11666400-11667200	Flanking Active TSS	HepG2	liver
25	chr8:11666400-11667400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr8:11666400-11669000	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr8:11666400-11670400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr8:11666400-11671400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:11666600-11667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr8:11666600-11667200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:11666600-11667200	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr8:11666600-11667200	Active TSS	Colonic Mucosa	Colon
33	chr8:11666600-11667200	Weak transcription	Esophagus	oesophagus
34	chr8:11666600-11667200	Weak transcription	Gastric	stomach
35	chr8:11666600-11667200	Weak transcription	Lung	lung
36	chr8:11666600-11667200	Weak transcription	Pancreas	Pancrea
37	chr8:11666600-11667200	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr8:11666600-11667400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:11666600-11667400	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
40	chr8:11666600-11667400	Genic enhancers	Spleen	Spleen
41	chr8:11666600-11667600	Flanking Active TSS	Fetal Lung	lung
42	chr8:11666600-11668000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr8:11666600-11668000	Genic enhancers	K562	blood
44	chr8:11666600-11669600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr8:11666600-11670400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr8:11666600-11671200	Weak transcription	Small Intestine	intestine
47	chr8:11666800-11667200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr8:11666800-11667200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr8:11666800-11667200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr8:11666800-11667200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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