Variant report

Variant	rs2303487
Chromosome Location	chr17:46704536-46704537
allele	G/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	chr17:46701823-46705617	K562	blood:	n/a	n/a
2	RCOR1	chr17:46703541-46704868	K562	blood:	n/a	n/a
3	BHLHE40	chr17:46703145-46704596	K562	blood:	n/a	n/a
4	POLR2A	chr17:46702158-46704945	K562	blood:	n/a	n/a
5	PML	chr17:46703480-46704688	K562	blood:	n/a	n/a
6	POLR2A	chr17:46701890-46705619	K562	blood:	n/a	n/a
7	IRF1	chr17:46703196-46704556	K562	blood:	n/a	n/a
8	NR2F2	chr17:46703609-46705155	K562	blood:	n/a	n/a
9	POLR2A	chr17:46701711-46705055	HCT-116	colon:	n/a	n/a
10	POLR2A	chr17:46702081-46704696	K562	blood:	n/a	n/a
11	ELK1	chr17:46703911-46704559	K562	blood:	n/a	n/a
12	JUN	chr17:46702956-46704714	K562	blood:	n/a	chr17:46703061-46703070
13	POLR2A	chr17:46692107-46708447	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr17:46701690-46705809	K562	blood:	n/a	n/a
15	EGR1	chr17:46702554-46704811	HCT-116	colon:	n/a	chr17:46704081-46704095 chr17:46704095-46704109 chr17:46702898-46702908 chr17:46704083-46704093 chr17:46703060-46703070 chr17:46703759-46703772 chr17:46704079-46704089 chr17:46704080-46704093 chr17:46702754-46702764 chr17:46704713-46704726 chr17:46704080-46704094 chr17:46704080-46704093 chr17:46704079-46704094 chr17:46704080-46704093 chr17:46704083-46704092
16	POLR2A	chr17:46695067-46708834	K562	blood:	n/a	n/a
17	TCF12	chr17:46701920-46704621	A549	lung:	n/a	n/a
18	POLR2A	chr17:46702919-46704696	K562	blood:	n/a	n/a
19	POLR2A	chr17:46703166-46704699	K562	blood:	n/a	n/a
20	POLR2A	chr17:46685805-46708856	PANC-1	pancreas:	n/a	n/a
21	HEY1	chr17:46702361-46704544	K562	blood:	n/a	chr17:46704077-46704092 chr17:46704080-46704095 chr17:46703893-46703908 chr17:46704027-46704042
22	TCF12	chr17:46704283-46704568	H1-hESC	embryonic stem cell:	n/a	n/a
23	YY1	chr17:46704356-46705033	K562	blood:	n/a	n/a
24	ZNF143	chr17:46703497-46704608	K562	blood:	n/a	n/a
25	ZMIZ1	chr17:46703178-46704939	K562	blood:	n/a	n/a
26	CUX1	chr17:46703759-46704642	K562	blood:	n/a	n/a
27	MAZ	chr17:46702137-46705806	K562	blood:	n/a	chr17:46703964-46703973 chr17:46703065-46703075 chr17:46703749-46703759 chr17:46704706-46704715
28	EGR1	chr17:46703638-46704544	HCT-116	colon:	n/a	chr17:46704081-46704095 chr17:46704095-46704109 chr17:46704083-46704093 chr17:46703759-46703772 chr17:46704079-46704089 chr17:46704080-46704093 chr17:46704080-46704094 chr17:46704080-46704093 chr17:46704079-46704094 chr17:46704080-46704093 chr17:46704083-46704092
29	SUZ12	chr17:46701854-46705033	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr17:46702244-46704660	HCT-116	colon:	n/a	n/a
31	HEY1	chr17:46704057-46704730	K562	blood:	n/a	chr17:46704077-46704092 chr17:46704080-46704095
32	POLR2A	chr17:46702318-46705449	K562	blood:	n/a	n/a
33	POLR2A	chr17:46701810-46705548	K562	blood:	n/a	n/a
34	ZNF263	chr17:46703826-46704583	HEK293-T-REx	kidney:	n/a	chr17:46704495-46704504
35	YY1	chr17:46704535-46704879	K562	blood:	n/a	n/a
36	BCL3	chr17:46702560-46705062	A549	lung:	n/a	chr17:46703060-46703073 chr17:46704079-46704092 chr17:46704077-46704086 chr17:46704080-46704089 chr17:46703678-46703687 chr17:46703740-46703753 chr17:46704086-46704095
37	RCOR1	chr17:46703345-46704749	K562	blood:	n/a	n/a
38	POLR2A	chr17:46702907-46704683	K562	blood:	n/a	n/a
39	REST	chr17:46704332-46704819	A549	lung:	n/a	chr17:46704491-46704504

No.	Distal block	Cell Line	Cell type
1	chr17:46701571..46706598-chr17:47072048..47076281,6	K562	blood:
2	chr17:46618868..46624573-chr17:46700689..46705978,10	K562	blood:
3	chr17:46702795..46705458-chr17:47072563..47074933,4	K562	blood:
4	chr17:46124778..46127532-chr17:46702734..46705232,2	K562	blood:
5	chr17:46685746..46689281-chr17:46702801..46705653,3	MCF-7	breast:
6	chr17:46686493..46690300-chr17:46702976..46707350,6	MCF-7	breast:

Variant related genes	Relation type
HOXB-AS4	TF binding region
HOXB9	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000173917	Chromatin interaction
ENSG00000230148	Chromatin interaction
ENSG00000260027	Chromatin interaction
ENSG00000250838	Chromatin interaction
ENSG00000159217	Chromatin interaction
ENSG00000263412	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1057201	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11652932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11652981	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12938558	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2326016	0.94[ASN][1000 genomes]
rs2875820	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3096649	1.00[YRI][hapmap]
rs3809775	0.94[ASN][1000 genomes]
rs3809780	0.93[ASN][1000 genomes]
rs4793598	0.81[AFR][1000 genomes]
rs4793963	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs731748	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs890435	0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9913020	0.82[EUR][1000 genomes]
rs9913026	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv543380	chr17:46686151-46721371	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2303487	CDK5RAP3	cis	parietal	SCAN
rs2303487	TTLL6	cis	cerebellum	SCAN
rs2303487	HOXB2	cis	cerebellum	SCAN
rs2303487	PNPO	cis	parietal	SCAN
rs2303487	UBE2Z	cis	parietal	SCAN
rs2303487	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46702000-46704600	Bivalent Enhancer	Fetal Thymus	thymus
2	chr17:46703000-46704600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:46703000-46704600	Bivalent Enhancer	Fetal Lung	lung
4	chr17:46703200-46704600	Bivalent Enhancer	Fetal Stomach	stomach
5	chr17:46703400-46704600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
6	chr17:46703600-46704600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
7	chr17:46703600-46704600	Bivalent Enhancer	Brain Hippocampus Middle	brain
8	chr17:46703600-46704600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
9	chr17:46703600-46704600	Bivalent Enhancer	Placenta	Placenta
10	chr17:46703600-46705000	Bivalent/Poised TSS	NHEK	skin
11	chr17:46703600-46705200	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr17:46703800-46704600	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:46703800-46704600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
14	chr17:46703800-46704800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
15	chr17:46703800-46705000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
16	chr17:46703800-46705200	Bivalent/Poised TSS	Small Intestine	intestine
17	chr17:46704000-46704600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr17:46704000-46704600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr17:46704000-46704600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
20	chr17:46704000-46704600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
21	chr17:46704000-46704600	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr17:46704000-46704600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr17:46704000-46704600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
24	chr17:46704000-46704600	Flanking Active TSS	A549	lung
25	chr17:46704000-46704600	Bivalent Enhancer	HUVEC	blood vessel
26	chr17:46704200-46704600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
27	chr17:46704200-46704600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr17:46704200-46704600	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
29	chr17:46704200-46704600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
30	chr17:46704200-46704600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:46704200-46704600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
32	chr17:46704200-46704600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:46704200-46704600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr17:46704200-46704600	Bivalent/Poised TSS	Fetal Kidney	kidney
35	chr17:46704200-46704600	Bivalent Enhancer	HSMMtube	muscle
36	chr17:46704200-46704800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
37	chr17:46704200-46705000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr17:46704200-46705000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
39	chr17:46704200-46705000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
40	chr17:46704400-46704600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
41	chr17:46704400-46704600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:46704400-46704600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
43	chr17:46704400-46704600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:46704400-46704600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr17:46704400-46704600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:46704400-46704600	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr17:46704400-46704600	Bivalent Enhancer	Fetal Intestine Small	intestine
48	chr17:46704400-46704600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
49	chr17:46704400-46704600	Flanking Active TSS	K562	blood
50	chr17:46704400-46704800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links