Variant report

Variant	rs9907987
Chromosome Location	chr17:46659228-46659229
allele	C/T
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	POLR2A	chr17:46659164-46660059	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr17:46659217-46660110	K562	blood:	n/a	n/a
3	HEY1	chr17:46659133-46660036	K562	blood:	n/a	chr17:46659586-46659601 chr17:46659197-46659212 chr17:46659594-46659609
4	POLR2A	chr17:46658660-46659907	ECC-1	luminal epithelium:	n/a	n/a
5	SUZ12	chr17:46657913-46660550	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr17:46659129-46659821	PANC-1	pancreas:	n/a	chr17:46659202-46659215
7	POLR2A	chr17:46658373-46660633	K562	blood:	n/a	n/a
8	POLR2A	chr17:46658932-46660085	HUVEC	blood vessel:	n/a	n/a
9	CTBP2	chr17:46658907-46659900	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr17:46658970-46660480	IMR90	lung:	n/a	n/a
11	UBTF	chr17:46658772-46660316	K562	blood:	n/a	n/a
12	POLR2A	chr17:46659153-46659802	GM12878	blood:	n/a	n/a
13	SUZ12	chr17:46653107-46661081	NT2-D1	testis:	n/a	n/a
14	POLR2A	chr17:46658948-46659737	K562	blood:	n/a	n/a
15	CCNT2	chr17:46658928-46659979	K562	blood:	n/a	n/a
16	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
17	ZBTB7A	chr17:46658650-46659250	K562	blood:	n/a	n/a
18	HMGN3	chr17:46658725-46659797	K562	blood:	n/a	n/a
19	SIN3AK20	chr17:46658652-46660393	PANC-1	pancreas:	n/a	n/a
20	TCF7L2	chr17:46658895-46659979	PANC-1	pancreas:	n/a	n/a
21	ELF1	chr17:46659041-46659950	GM12878	blood:	n/a	chr17:46659599-46659608 chr17:46659594-46659606 chr17:46659596-46659605 chr17:46659756-46659765
22	CHD1	chr17:46655927-46662288	IMR90	lung:	n/a	chr17:46657663-46657673 chr17:46660648-46660658
23	MTA3	chr17:46659209-46660037	GM12878	blood:	n/a	n/a
24	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46459433..46462163-chr17:46658202..46660838,2	K562	blood:
2	chr17:46525263..46527446-chr17:46657806..46659592,2	K562	blood:
3	chr17:46652243..46654179-chr17:46657727..46659805,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HOXB4-1	chr17:46656992-46659621	ENSG00000257178.1

Variant related genes	Relation type
HOXB3	TF binding region
HOXB4	TF binding region
MIR10A	TF binding region
ENSG00000200538	Chromatin interaction
ENSG00000120093	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10853101	0.84[JPT][hapmap]
rs11652148	0.92[CHB][hapmap]
rs1553755	0.81[GIH][hapmap]
rs2288276	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2288277	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2288278	0.92[JPT][hapmap]
rs2288279	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555109	0.95[ASN][1000 genomes]
rs2740752	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.97[ASN][1000 genomes]
rs3809782	0.84[JPT][hapmap]
rs4646992	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6504389	0.92[CHB][hapmap]
rs6504397	0.80[ASW][hapmap]
rs6504411	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs733920	0.92[CHB][hapmap]
rs7405452	0.89[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7406170	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7406798	0.80[ASW][hapmap]
rs7406910	0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs7503053	0.92[CHB][hapmap]
rs890431	0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs9221	0.91[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9903182	0.82[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9905793	0.92[AMR][1000 genomes];0.98[EUR][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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	nsv908577	chr17:46584900-46704536	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	343 gene(s)	inside rSNPs	diseases
4	nsv908578	chr17:46592413-46698710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
5	nsv908579	chr17:46592413-46727289	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
6	nsv532113	chr17:46598247-47588570	Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	453 gene(s)	inside rSNPs	diseases
7	esv2758459	chr17:46602673-46836837	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
8	esv2758694	chr17:46602673-46836837	Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	364 gene(s)	inside rSNPs	diseases
9	nsv908580	chr17:46609103-46698710	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	335 gene(s)	inside rSNPs	diseases
10	nsv908581	chr17:46610646-46735520	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
11	nsv575480	chr17:46617019-46684929	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
12	nsv908582	chr17:46617019-46698710	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
13	nsv908583	chr17:46617019-46704536	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
14	nsv833471	chr17:46617787-46783345	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	356 gene(s)	inside rSNPs	diseases
15	nsv908584	chr17:46618926-46735520	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
16	nsv457822	chr17:46620402-46698710	Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
17	nsv575481	chr17:46620402-46698710	Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
18	nsv457823	chr17:46620402-46704536	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
19	nsv575482	chr17:46620402-46704536	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	342 gene(s)	inside rSNPs	diseases
20	nsv457824	chr17:46625519-46693491	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
21	nsv575483	chr17:46625519-46693491	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46653400-46660400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr17:46653600-46660200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:46656000-46660600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr17:46656000-46661200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr17:46657800-46659600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr17:46657800-46660200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr17:46658000-46659800	Bivalent/Poised TSS	Lung	lung
8	chr17:46658000-46661000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
9	chr17:46658200-46660000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
10	chr17:46658200-46660000	Weak transcription	A549	lung
11	chr17:46658400-46659400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr17:46658400-46661800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr17:46658600-46659400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:46658600-46659400	Flanking Active TSS	Colonic Mucosa	Colon
15	chr17:46658600-46659400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
16	chr17:46658600-46659600	Bivalent/Poised TSS	NHEK	skin
17	chr17:46658600-46659800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
18	chr17:46658600-46659800	Active TSS	HSMM	muscle
19	chr17:46658600-46660000	Bivalent/Poised TSS	Psoas Muscle	Psoas
20	chr17:46658600-46660200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:46658800-46659400	Active TSS	Pancreas	Pancrea
22	chr17:46658800-46659400	Active TSS	Right Atrium	heart
23	chr17:46658800-46659600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
24	chr17:46658800-46659600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr17:46658800-46659600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:46658800-46659600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr17:46658800-46659600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
28	chr17:46658800-46659600	Active TSS	Stomach Smooth Muscle	stomach
29	chr17:46658800-46659800	Active TSS	Aorta	Aorta
30	chr17:46658800-46659800	Active TSS	Esophagus	oesophagus
31	chr17:46658800-46659800	Active TSS	K562	blood
32	chr17:46658800-46660000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:46658800-46660000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr17:46658800-46660000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
35	chr17:46658800-46660000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr17:46658800-46660000	Bivalent Enhancer	Fetal Thymus	thymus
37	chr17:46658800-46660200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr17:46658800-46660200	Active TSS	Colon Smooth Muscle	Colon
39	chr17:46658800-46660200	Transcr. at gene 5' and 3'	NHLF	lung
40	chr17:46658800-46660400	Active TSS	NHDF-Ad	bronchial
41	chr17:46658800-46660600	Active TSS	Fetal Kidney	kidney
42	chr17:46658800-46665800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:46659000-46659400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:46659000-46659400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr17:46659000-46659400	Bivalent Enhancer	Primary B cells from cord blood	blood
46	chr17:46659000-46659400	Flanking Active TSS	GM12878-XiMat	blood
47	chr17:46659000-46659600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
48	chr17:46659000-46659600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
49	chr17:46659000-46659600	Active TSS	Spleen	Spleen
50	chr17:46659000-46659800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin

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