Variant report

Variant	rs8066692
Chromosome Location	chr17:15554278-15554279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr17:15554130-15555513	ECC-1	luminal epithelium:	n/a	chr17:15554331-15554347
2	POLR2A	chr17:15553120-15555494	MCF10A-Er-Src	breast:	n/a	n/a
3	ELF1	chr17:15553937-15555363	A549	lung:	n/a	n/a
4	TCF12	chr17:15552877-15555623	A549	lung:	n/a	chr17:15554340-15554347
5	GTF2F1	chr17:15554188-15555428	Hela-S3	cervix:	n/a	n/a
6	FOSL2	chr17:15552988-15555470	A549	lung:	n/a	chr17:15553338-15553348 chr17:15553338-15553348 chr17:15553338-15553348 chr17:15553340-15553351 chr17:15553338-15553347 chr17:15553338-15553348
7	PBX3	chr17:15554063-15555493	A549	lung:	n/a	n/a
8	BCL3	chr17:15553870-15555356	A549	lung:	n/a	n/a
9	ETS1	chr17:15554144-15555346	A549	lung:	n/a	n/a
10	MAX	chr17:15554029-15555520	HCT-116	colon:	n/a	chr17:15555238-15555249 chr17:15555238-15555249 chr17:15555237-15555250 chr17:15555238-15555249 chr17:15555234-15555253 chr17:15555239-15555248 chr17:15555237-15555250 chr17:15555238-15555247 chr17:15555239-15555249 chr17:15555237-15555250 chr17:15555239-15555249
11	CTCF	chr17:15554220-15554370	AG09309	skin:	n/a	n/a
12	STAT3	chr17:15552888-15554330	MCF10A-Er-Src	breast:	n/a	chr17:15553338-15553347 chr17:15553945-15553956 chr17:15553661-15553675 chr17:15553738-15553745 chr17:15553452-15553475 chr17:15553664-15553673 chr17:15553663-15553672
13	MAFK	chr17:15554050-15555459	Hela-S3	cervix:	n/a	n/a
14	SP1	chr17:15554069-15555461	A549	lung:	n/a	n/a
15	POLR2A	chr17:15554260-15555445	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:15554268-15554598	A549	lung:	n/a	n/a
17	SP1	chr17:15554054-15555494	A549	lung:	n/a	n/a
18	CEBPB	chr17:15553130-15554490	Hela-S3	cervix:	n/a	n/a
19	HDAC2	chr17:15554168-15555420	MCF-7	breast:	n/a	chr17:15555334-15555348
20	POLR2A	chr17:15554181-15555409	MCF-7	breast:	n/a	n/a
21	BCL3	chr17:15554150-15555483	A549	lung:	n/a	n/a
22	POLR2A	chr17:15554047-15554613	Hela-S3	cervix:	n/a	n/a
23	ELK1	chr17:15554093-15554627	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr17:15554234-15555394	A549	lung:	n/a	n/a
25	USF2	chr17:15554118-15555444	Hela-S3	cervix:	n/a	chr17:15555237-15555248
26	PBX3	chr17:15554085-15555247	A549	lung:	n/a	n/a
27	NFIC	chr17:15554269-15555469	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr17:15554068-15555402	A549	lung:	n/a	chr17:15554331-15554347
29	MAX	chr17:15554024-15555433	Hela-S3	cervix:	n/a	chr17:15555238-15555249 chr17:15555238-15555249 chr17:15555237-15555250 chr17:15555238-15555249 chr17:15555234-15555253 chr17:15555239-15555248 chr17:15555237-15555250 chr17:15555238-15555247 chr17:15555239-15555249 chr17:15555237-15555250 chr17:15555239-15555249
30	POLR2A	chr17:15554263-15554645	A549	lung:	n/a	n/a
31	NFIC	chr17:15552980-15554475	ECC-1	luminal epithelium:	n/a	chr17:15553980-15553997 chr17:15553981-15553997
32	RAD21	chr17:15554182-15555369	IMR90	lung:	n/a	chr17:15554362-15554374
33	SIN3AK20	chr17:15554007-15555500	MCF-7	breast:	n/a	n/a
34	SMC3	chr17:15554153-15555413	Hela-S3	cervix:	n/a	n/a
35	EP300	chr17:15554128-15555433	A549	lung:	n/a	chr17:15554331-15554347
36	MAX	chr17:15554267-15555498	ECC-1	luminal epithelium:	n/a	chr17:15555238-15555249 chr17:15555238-15555249 chr17:15555237-15555250 chr17:15555238-15555249 chr17:15555234-15555253 chr17:15555239-15555248 chr17:15555237-15555250 chr17:15555238-15555247 chr17:15555239-15555249 chr17:15555237-15555250 chr17:15555239-15555249
37	E2F6	chr17:15554184-15555526	A549	lung:	n/a	n/a
38	POLR2A	chr17:15553192-15555481	MCF10A-Er-Src	breast:	n/a	n/a
39	GATA3	chr17:15554056-15555527	A549	lung:	n/a	n/a
40	POLR2A	chr17:15554216-15555499	U87	brain:	n/a	n/a
41	POLR2A	chr17:15554018-15555341	ECC-1	luminal epithelium:	n/a	n/a
42	MAX	chr17:15554248-15555458	MCF-7	breast:	n/a	chr17:15555238-15555249 chr17:15555238-15555249 chr17:15555237-15555250 chr17:15555238-15555249 chr17:15555234-15555253 chr17:15555239-15555248 chr17:15555237-15555250 chr17:15555238-15555247 chr17:15555239-15555249 chr17:15555237-15555250 chr17:15555239-15555249
43	POLR2A	chr17:15554250-15554370	Hela-S3	cervix:	n/a	n/a
44	SIN3AK20	chr17:15554134-15555447	A549	lung:	n/a	n/a
45	SIN3AK20	chr17:15553963-15555495	A549	lung:	n/a	n/a
46	MAX	chr17:15552793-15555516	A549	lung:	n/a	chr17:15555238-15555249 chr17:15555238-15555249 chr17:15553339-15553348 chr17:15555237-15555250 chr17:15555238-15555249 chr17:15555234-15555253 chr17:15555239-15555248 chr17:15555237-15555250 chr17:15555238-15555247 chr17:15555239-15555249 chr17:15555237-15555250 chr17:15555239-15555249
47	POLR2A	chr17:15554098-15555466	MCF-7	breast:	n/a	n/a
48	MXI1	chr17:15553449-15555638	SK-N-SH	brain:	n/a	chr17:15555238-15555247 chr17:15555240-15555249
49	RCOR1	chr17:15554173-15555389	Hela-S3	cervix:	n/a	n/a
50	TAF1	chr17:15554277-15555463	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:15553842..15556755-chr17:15901183..15904132,3	MCF-7	breast:
2	chr17:15552019..15554730-chr17:16119203..16121978,2	MCF-7	breast:
3	chr17:15551872..15554786-chr17:16116224..16118866,3	MCF-7	breast:
4	chr17:15553526..15556124-chr17:15902249..15904435,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266261	TF binding region
ENSG00000011295	Chromatin interaction
ENSG00000108474	Chromatin interaction
ENSG00000141027	Chromatin interaction
ENSG00000214941	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10521309	0.90[MEX][hapmap]
rs1476728	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3760302	0.90[MEX][hapmap]
rs3785634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3785635	0.90[MEX][hapmap]
rs3785642	0.90[MEX][hapmap]
rs4792637	1.00[CHB][hapmap]
rs4792642	0.84[MEX][hapmap]
rs4792643	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4792644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58806844	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7213827	0.90[MEX][hapmap]
rs7223394	0.90[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv457695	chr17:15447364-15611495	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv574462	chr17:15447364-15611495	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1067123	chr17:15482503-15557728	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv907704	chr17:15542933-15567196	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8066692	PMP22	cis	multi-tissue	Pritchard
rs8066692	TRIM16	cis	lymphoblastoid	seeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15549600-15554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr17:15549600-15554400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:15549600-15554400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr17:15549600-15554800	Weak transcription	GM12878-XiMat	blood
5	chr17:15550000-15554600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:15551000-15554400	Active TSS	Esophagus	oesophagus
7	chr17:15551600-15554400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr17:15551600-15555000	Active TSS	Psoas Muscle	Psoas
9	chr17:15551600-15555000	Flanking Active TSS	Hela-S3	cervix
10	chr17:15552200-15554400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr17:15552200-15555200	Active TSS	Stomach Mucosa	stomach
12	chr17:15552200-15564600	Weak transcription	HepG2	liver
13	chr17:15552400-15554400	Active TSS	Right Ventricle	heart
14	chr17:15552400-15555600	Active TSS	A549	lung
15	chr17:15552400-15555600	Active TSS	HSMM	muscle
16	chr17:15552400-15555600	Active TSS	HSMMtube	muscle
17	chr17:15553000-15554600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:15553000-15554600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr17:15553000-15554600	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr17:15553000-15555000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:15553000-15555000	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr17:15553000-15555000	Flanking Active TSS	HMEC	breast
23	chr17:15553000-15555400	Flanking Active TSS	HUVEC	blood vessel
24	chr17:15553000-15555600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:15553000-15555600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr17:15553000-15555600	Flanking Active TSS	Osteobl	bone
27	chr17:15553200-15554400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr17:15553200-15554400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr17:15553200-15554800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr17:15553200-15555000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:15553200-15555000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr17:15553200-15555000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr17:15553200-15555400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr17:15553200-15555400	Flanking Active TSS	Fetal Lung	lung
35	chr17:15553200-15555400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr17:15553200-15555600	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr17:15553400-15554400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr17:15553400-15554400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr17:15553400-15554600	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr17:15553400-15555000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:15553400-15555000	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr17:15553400-15555200	Active TSS	Fetal Intestine Small	intestine
43	chr17:15553400-15555200	Active TSS	NHEK	skin
44	chr17:15553400-15555600	Active TSS	Aorta	Aorta
45	chr17:15553600-15554400	Active TSS	Fetal Kidney	kidney
46	chr17:15553600-15554400	Active TSS	Fetal Thymus	thymus
47	chr17:15553600-15554600	Enhancers	Liver	Liver
48	chr17:15553600-15554800	Enhancers	Primary hematopoietic stem cells	blood
49	chr17:15553600-15555000	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr17:15553600-15555200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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