Variant report

Variant	rs883541
Chromosome Location	chr17:66449122-66449123
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr17:66449037-66449357	T-47D	breast:	n/a	n/a
2	POLR2A	chr17:66449027-66449301	H1-neurons	neurons:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:66431094..66434502-chr17:66448971..66451470,3	MCF-7	breast:
2	chr17:66254604..66256294-chr17:66447606..66449593,2	MCF-7	breast:
3	chr17:66242541..66245754-chr17:66448578..66451592,3	MCF-7	breast:
4	chr17:66445448..66449611-chr17:66450414..66454852,7	K562	blood:
5	chr17:66447605..66450395-chr17:66509895..66512171,2	MCF-7	breast:

No data

Variant related genes	Relation type
WIPI1	TF binding region
ENSG00000196704	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000070540	Chromatin interaction
ENSG00000108946	Chromatin interaction
ENSG00000265100	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11868680	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.80[ASN][1000 genomes]
rs1808335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111508	0.86[ASN][1000 genomes]
rs2302783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909207	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs2909209	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2909211	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909213	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2909216	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2909217	0.88[ASN][1000 genomes]
rs2909218	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs2909220	0.82[ASN][1000 genomes]
rs2909221	0.81[ASN][1000 genomes]
rs2952279	0.88[TSI][hapmap]
rs2952289	0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2952290	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2952294	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952295	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2952296	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6501468	0.94[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs71378928	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8072338	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833523	chr17:66343323-66510461	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs883541	TANC2	cis	cerebellum	SCAN
rs883541	STRADA	cis	parietal	SCAN
rs883541	PRKAR1A	cis	multi-tissue	Pritchard
rs883541	CD79B	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66410400-66452400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:66420800-66451800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr17:66425400-66451600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:66425400-66452000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr17:66432200-66452400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:66432600-66451600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:66433000-66451800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr17:66433000-66451800	Weak transcription	Hela-S3	cervix
9	chr17:66434400-66450200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr17:66434600-66450400	Strong transcription	Osteobl	bone
11	chr17:66434800-66452200	Weak transcription	Dnd41	blood
12	chr17:66434800-66452400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr17:66434800-66452600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:66435200-66452200	Weak transcription	Stomach Mucosa	stomach
15	chr17:66435600-66449400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr17:66437200-66451600	Weak transcription	GM12878-XiMat	blood
17	chr17:66437400-66451600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr17:66437400-66451600	Weak transcription	Small Intestine	intestine
19	chr17:66437600-66452800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:66437800-66449200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:66438000-66449200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:66438000-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr17:66438200-66449800	Weak transcription	Fetal Lung	lung
24	chr17:66438200-66452000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:66438200-66452000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr17:66438200-66452400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:66438400-66452400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr17:66438400-66452400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:66438600-66449200	Strong transcription	Lung	lung
30	chr17:66438800-66449400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr17:66439000-66450400	Weak transcription	Primary B cells from cord blood	blood
32	chr17:66439200-66449400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr17:66439600-66449400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr17:66441800-66449200	Weak transcription	Fetal Heart	heart
35	chr17:66441800-66449200	Strong transcription	NHDF-Ad	bronchial
36	chr17:66442600-66449400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:66442600-66449400	Strong transcription	HSMM	muscle
38	chr17:66443000-66449200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr17:66443000-66449400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:66443200-66449200	Strong transcription	Left Ventricle	heart
41	chr17:66443200-66452200	Weak transcription	Fetal Brain Female	brain
42	chr17:66443800-66449800	Weak transcription	A549	lung
43	chr17:66443800-66452200	Weak transcription	Fetal Brain Male	brain
44	chr17:66444200-66449200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr17:66444600-66449400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:66445800-66451600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr17:66446000-66451800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:66446800-66451600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr17:66446800-66452800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr17:66447000-66451600	Genic enhancers	HepG2	liver

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