Variant report

Variant	rs12951076
Chromosome Location	chr17:46625109-46625110
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	chr17:46620117-46628421	PANC-1	pancreas:	n/a	n/a
2	KAP1	chr17:46623982-46625541	HEK293	kidney:	n/a	n/a
3	POLR2A	chr17:46616545-46629919	PANC-1	pancreas:	n/a	n/a
4	ESR1	chr17:46624850-46625202	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr17:46623587-46626234	K562	blood:	n/a	n/a
6	TEAD4	chr17:46624774-46625300	ECC-1	luminal epithelium:	n/a	n/a
7	NR2F2	chr17:46624977-46626099	K562	blood:	n/a	n/a
8	GATA1	chr17:46623454-46626306	PBDE	blood:	n/a	n/a
9	CUX1	chr17:46624454-46625622	K562	blood:	n/a	n/a
10	TCF7L2	chr17:46623886-46625674	HEK293	kidney:	n/a	n/a
11	TCF7L2	chr17:46623685-46625686	PANC-1	pancreas:	n/a	chr17:46623782-46623798 chr17:46623782-46623798
12	ESR1	chr17:46624290-46625199	T-47D	breast:	n/a	n/a
13	KAP1	chr17:46624241-46625575	U2OS	brain:	n/a	n/a
14	NFIC	chr17:46624668-46625340	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr17:46625076-46625985	HUVEC	blood vessel:	n/a	n/a
16	NFIC	chr17:46624487-46625373	ECC-1	luminal epithelium:	n/a	n/a
17	RCOR1	chr17:46625088-46625404	K562	blood:	n/a	n/a
18	POLR2A	chr17:46620299-46626078	K562	blood:	n/a	n/a
19	CEBPB	chr17:46625079-46625396	K562	blood:	n/a	chr17:46625254-46625265 chr17:46625254-46625267
20	POLR2A	chr17:46624931-46626263	K562	blood:	n/a	n/a
21	EP300	chr17:46623582-46626390	K562	blood:	n/a	chr17:46623675-46623689 chr17:46625690-46625704 chr17:46624914-46624928 chr17:46624292-46624302 chr17:46624922-46624936 chr17:46625689-46625703 chr17:46624928-46624942 chr17:46623604-46623612
22	EP300	chr17:46624239-46625117	T-47D	breast:	n/a	chr17:46624914-46624928 chr17:46624292-46624302 chr17:46624922-46624936 chr17:46624928-46624942
23	POLR2A	chr17:46622500-46628313	K562	blood:	n/a	n/a
24	FOXM1	chr17:46624714-46625348	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr17:46623933-46625651	PBDE	blood:	n/a	n/a
26	MAFK	chr17:46624958-46625594	K562	blood:	n/a	n/a
27	POLR2A	chr17:46623771-46625637	K562	blood:	n/a	n/a
28	GATA3	chr17:46624229-46625206	T-47D	breast:	n/a	chr17:46624469-46624477
29	ESR1	chr17:46624141-46625215	T-47D	breast:	n/a	n/a
30	IRF1	chr17:46624090-46626016	K562	blood:	n/a	chr17:46625169-46625179 chr17:46624927-46624937 chr17:46625168-46625180 chr17:46625169-46625183 chr17:46624618-46624632 chr17:46624927-46624941 chr17:46625165-46625179 chr17:46625680-46625694 chr17:46624923-46624937
31	TBL1XR1	chr17:46623343-46626410	K562	blood:	n/a	n/a
32	TBL1XR1	chr17:46625056-46625307	K562	blood:	n/a	n/a
33	POLR2A	chr17:46625091-46625529	H1-neurons	neurons:	n/a	n/a
34	ESR1	chr17:46624223-46625203	T-47D	breast:	n/a	n/a
35	ESR1	chr17:46624801-46625321	ECC-1	luminal epithelium:	n/a	n/a
36	EP300	chr17:46624273-46625441	ECC-1	luminal epithelium:	n/a	chr17:46624914-46624928 chr17:46624292-46624302 chr17:46624922-46624936 chr17:46624928-46624942
37	PML	chr17:46625077-46625971	K562	blood:	n/a	n/a
38	POLR2A	chr17:46624910-46625185	ECC-1	luminal epithelium:	n/a	n/a
39	IRF1	chr17:46623456-46625835	K562	blood:	n/a	chr17:46623678-46623691 chr17:46625169-46625179 chr17:46624927-46624937 chr17:46625168-46625180 chr17:46623676-46623690 chr17:46625169-46625183 chr17:46624618-46624632 chr17:46624927-46624941 chr17:46625165-46625179 chr17:46625680-46625694 chr17:46624923-46624937 chr17:46623680-46623690
40	TEAD4	chr17:46625090-46626108	K562	blood:	n/a	n/a
41	TCF12	chr17:46624730-46625447	ECC-1	luminal epithelium:	n/a	n/a
42	TEAD4	chr17:46624933-46625928	K562	blood:	n/a	n/a
43	ARID3A	chr17:46624385-46626253	K562	blood:	n/a	n/a
44	GATA3	chr17:46624224-46625153	T-47D	breast:	n/a	chr17:46624469-46624477

Variant related genes	Relation type
HOXB-AS3	TF binding region
HOXB2	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1042818	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1042822	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1062037	0.98[AMR][1000 genomes]
rs11868098	0.84[EUR][1000 genomes]
rs12602539	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12603976	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12938390	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12939811	0.93[EUR][1000 genomes]
rs12946855	0.88[EUR][1000 genomes]
rs12946931	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs12947405	0.97[EUR][1000 genomes]
rs17703636	0.83[EUR][1000 genomes]
rs17703660	0.83[EUR][1000 genomes]
rs2229302	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2326012	0.97[EUR][1000 genomes]
rs34378400	0.87[EUR][1000 genomes]
rs34490194	0.90[AMR][1000 genomes]
rs34822124	0.93[AMR][1000 genomes]
rs35621842	0.92[EUR][1000 genomes]
rs35624684	0.85[AMR][1000 genomes]
rs35825473	0.98[AMR][1000 genomes]
rs4793889	0.87[EUR][1000 genomes]
rs55859232	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56038617	0.95[EUR][1000 genomes]
rs56115209	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56128659	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62065846	0.88[EUR][1000 genomes]
rs62066689	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62066693	0.97[EUR][1000 genomes]
rs6504340	0.90[EUR][1000 genomes]
rs67412921	0.98[AMR][1000 genomes]
rs7207109	0.88[EUR][1000 genomes]
rs7222242	0.83[EUR][1000 genomes]
rs7225995	0.88[EUR][1000 genomes]
rs8064626	0.83[EUR][1000 genomes]
rs8066613	0.87[EUR][1000 genomes]
rs8071207	0.81[EUR][1000 genomes]
rs8072250	0.82[EUR][1000 genomes]
rs8073963	0.88[EUR][1000 genomes]
rs8074125	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs8079617	0.95[EUR][1000 genomes]
rs9904760	0.84[EUR][1000 genomes]
rs9905940	0.90[EUR][1000 genomes]
rs9906950	0.80[EUR][1000 genomes]
rs9989493	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12951076	HOXB2	cis	Adipose Subcutaneous	GTEx
rs12951076	HOXB2	cis	lung	GTEx
rs12951076	HOXB2	cis	Whole Blood	GTEx
rs12951076	HOXB-AS1	cis	Whole Blood	GTEx

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46618800-46625600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46621200-46629600	Weak transcription	Gastric	stomach
3	chr17:46621600-46628000	Weak transcription	Pancreas	Pancrea
4	chr17:46621600-46634400	Weak transcription	Hela-S3	cervix
5	chr17:46621800-46627600	Weak transcription	Spleen	Spleen
6	chr17:46622000-46625400	Weak transcription	Small Intestine	intestine
7	chr17:46622000-46626200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:46622400-46625400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:46622400-46625600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:46622400-46625600	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr17:46622400-46626200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:46622400-46626600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr17:46622600-46625200	Flanking Active TSS	K562	blood
14	chr17:46622600-46626200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr17:46622800-46627400	Weak transcription	Placenta	Placenta
16	chr17:46623200-46627400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr17:46623600-46625200	Enhancers	A549	lung
18	chr17:46623600-46625600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr17:46623600-46625600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:46623800-46625200	Flanking Active TSS	NHLF	lung
21	chr17:46623800-46625600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr17:46623800-46625600	Enhancers	Colonic Mucosa	Colon
23	chr17:46623800-46625600	Flanking Active TSS	Fetal Stomach	stomach
24	chr17:46623800-46626200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:46623800-46630800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:46624000-46625200	Active TSS	Colon Smooth Muscle	Colon
27	chr17:46624000-46625400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr17:46624000-46625400	Active TSS	Aorta	Aorta
29	chr17:46624000-46625400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr17:46624000-46625400	Active TSS	Right Atrium	heart
31	chr17:46624000-46625600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr17:46624000-46625600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr17:46624000-46625600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr17:46624000-46625600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr17:46624000-46625800	Flanking Active TSS	HUVEC	blood vessel
36	chr17:46624000-46626200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr17:46624000-46629800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
38	chr17:46624200-46625400	Bivalent Enhancer	Thymus	Thymus
39	chr17:46624200-46625600	Flanking Active TSS	Primary T cells from cord blood	blood
40	chr17:46624200-46625600	Active TSS	Rectal Mucosa Donor 29	rectum
41	chr17:46624200-46626800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr17:46624400-46625200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
43	chr17:46624400-46625600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr17:46624400-46626600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
45	chr17:46624400-46627000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr17:46624400-46627400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr17:46624600-46625200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
48	chr17:46624600-46625200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr17:46624600-46625200	Bivalent Enhancer	Fetal Intestine Small	intestine
50	chr17:46624600-46625200	Active TSS	Fetal Muscle Trunk	muscle

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