Variant report

Variant	rs4985778
Chromosome Location	chr17:16922378-16922379
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	SIN3AK20	chr17:16921789-16922575	MCF-7	breast:	n/a	n/a
2	NR3C1	chr17:16921764-16922558	A549	lung:	n/a	chr17:16922260-16922273 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922061-16922076 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922057-16922078
3	NFIC	chr17:16921772-16922489	ECC-1	luminal epithelium:	n/a	n/a
4	MAX	chr17:16921557-16922531	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr17:16921456-16922833	ECC-1	luminal epithelium:	n/a	chr17:16921474-16921481
6	TEAD4	chr17:16921822-16922542	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr17:16921813-16922485	ECC-1	luminal epithelium:	n/a	n/a
8	NR2F2	chr17:16921822-16922513	MCF-7	breast:	n/a	n/a
9	EP300	chr17:16921768-16922426	MCF-7	breast:	n/a	n/a
10	GATA3	chr17:16921876-16922450	MCF-7	breast:	n/a	n/a
11	NR3C1	chr17:16921819-16922440	A549	lung:	n/a	chr17:16922260-16922273 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922061-16922076 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922057-16922078
12	ZBTB7A	chr17:16921832-16922622	ECC-1	luminal epithelium:	n/a	n/a
13	NR2F2	chr17:16921824-16922424	MCF-7	breast:	n/a	n/a
14	NR3C1	chr17:16921854-16922417	ECC-1	luminal epithelium:	n/a	chr17:16922260-16922273 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922061-16922076 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922057-16922078
15	MAX	chr17:16921710-16922474	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr17:16921765-16922511	MCF-7	breast:	n/a	n/a
17	YY1	chr17:16921855-16922378	ECC-1	luminal epithelium:	n/a	n/a
18	NR3C1	chr17:16921891-16922432	ECC-1	luminal epithelium:	n/a	chr17:16922260-16922273 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922061-16922076 chr17:16922055-16922081 chr17:16922061-16922075 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922055-16922081 chr17:16922060-16922076 chr17:16922060-16922076 chr17:16922057-16922078
19	MAX	chr17:16921618-16922585	MCF-7	breast:	n/a	n/a
20	HDAC2	chr17:16921813-16922501	MCF-7	breast:	n/a	chr17:16922471-16922490
21	TCF12	chr17:16921580-16922626	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr17:16921748-16922445	ECC-1	luminal epithelium:	n/a	n/a
23	NFIC	chr17:16921769-16922516	ECC-1	luminal epithelium:	n/a	n/a
24	HDAC2	chr17:16921880-16922437	MCF-7	breast:	n/a	n/a
25	EP300	chr17:16921430-16922538	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:16920777..16926602-chr17:16943525..16948995,8	MCF-7	breast:
2	chr17:16922009..16924326-chr17:16949178..16951661,2	MCF-7	breast:
3	chr17:16921692..16923812-chr17:17738364..17740042,2	MCF-7	breast:
4	chr17:16920975..16923605-chr17:16945817..16947937,2	K562	blood:
5	chr17:16919740..16922736-chr17:16924450..16926205,2	MCF-7	breast:
6	chr17:16921667..16924582-chr17:17139472..17141116,2	MCF-7	breast:
7	chr17:16920470..16922796-chr17:16981423..16984163,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260328	TF binding region
ENSG00000133030	Chromatin interaction
ENSG00000154803	Chromatin interaction
ENSG00000264187	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10852847	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11078374	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11656868	1.00[CHB][hapmap]
rs11871902	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090018	1.00[ASN][1000 genomes]
rs2271520	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2349646	1.00[ASN][1000 genomes]
rs28461224	1.00[ASN][1000 genomes]
rs4247118	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4247120	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4275914	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4514740	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985696	1.00[ASN][1000 genomes]
rs4985701	1.00[ASN][1000 genomes]
rs4985702	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985717	1.00[ASN][1000 genomes]
rs4985718	0.80[EUR][1000 genomes]
rs4985740	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4985746	1.00[ASN][1000 genomes]
rs6502563	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7206981	1.00[ASN][1000 genomes]
rs7207485	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208929	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7208973	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7217091	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7221842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7222311	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064550	1.00[ASN][1000 genomes]
rs8072184	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8073842	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8079563	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9893911	1.00[ASN][1000 genomes]
rs9898995	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9908767	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9914671	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv962271	chr17:16912264-16922846	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16906800-16923400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:16915000-16923600	Weak transcription	HSMMtube	muscle
3	chr17:16917400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:16917400-16926200	Enhancers	Stomach Mucosa	stomach
5	chr17:16918000-16926200	Enhancers	Placenta	Placenta
6	chr17:16918600-16924200	Weak transcription	Osteobl	bone
7	chr17:16918800-16923200	Weak transcription	HSMM	muscle
8	chr17:16918800-16924200	Enhancers	Hela-S3	cervix
9	chr17:16918800-16924200	Weak transcription	K562	blood
10	chr17:16918800-16930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:16919000-16922800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr17:16919000-16924200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr17:16919200-16923600	Weak transcription	Brain Anterior Caudate	brain
14	chr17:16919200-16924200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr17:16919200-16924200	Weak transcription	Small Intestine	intestine
16	chr17:16919800-16926200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:16920200-16922600	Enhancers	Gastric	stomach
18	chr17:16920200-16923600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr17:16920200-16926200	Enhancers	Pancreas	Pancrea
20	chr17:16920400-16923800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr17:16921000-16923800	Enhancers	Esophagus	oesophagus
22	chr17:16921000-16923800	Enhancers	NHEK	skin
23	chr17:16921000-16924200	Enhancers	Lung	lung
24	chr17:16921000-16924400	Enhancers	Fetal Intestine Small	intestine
25	chr17:16921000-16926200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:16921200-16922400	Enhancers	Spleen	Spleen
27	chr17:16921200-16923400	Enhancers	Fetal Thymus	thymus
28	chr17:16921200-16924200	Enhancers	Fetal Intestine Large	intestine
29	chr17:16921200-16925400	Enhancers	HMEC	breast
30	chr17:16921400-16922400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr17:16921400-16924800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr17:16921600-16922400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr17:16921600-16922600	Enhancers	Fetal Lung	lung
34	chr17:16921800-16924200	Enhancers	A549	lung
35	chr17:16922000-16922400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:16922200-16922400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr17:16922200-16923600	Enhancers	HepG2	liver
38	chr17:16922200-16924400	Weak transcription	H1 Cell Line	embryonic stem cell

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