Variant report

Variant	rs2740752
Chromosome Location	chr17:46664608-46664609
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	CHD1	chr17:46662335-46676284	IMR90	lung:	n/a	chr17:46662455-46662465 chr17:46670083-46670093 chr17:46669891-46669901
2	SUZ12	chr17:46662649-46665098	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr17:46655911-46684927	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr17:46645331-46684907	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46569552..46570496-chr17:46664083..46664942,2	K562	blood:
2	chr17:46663918..46665651-chr17:46666465..46668696,2	K562	blood:
3	chr17:46639764..46641981-chr17:46663009..46664957,2	MCF-7	breast:
4	chr17:46335792..46337533-chr17:46664070..46666326,2	K562	blood:
5	chr17:46572626..46574764-chr17:46662731..46664611,2	MCF-7	breast:
6	chr17:46663028..46666157-chr17:46668975..46671535,3	MCF-7	breast:

Variant related genes	Relation type
MIR10A	TF binding region
HOXB3	TF binding region
HOXB-AS3	TF binding region
ENSG00000120075	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10853101	0.84[JPT][hapmap]
rs11652148	0.83[CHB][hapmap]
rs2288276	0.89[ASN][1000 genomes]
rs2288277	0.92[CHB][hapmap]
rs2288278	0.92[JPT][hapmap]
rs2288279	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.97[ASN][1000 genomes]
rs2555109	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809782	0.84[JPT][hapmap]
rs6504389	0.83[CHB][hapmap]
rs6504411	0.89[ASN][1000 genomes]
rs733920	0.83[CHB][hapmap]
rs7405452	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs7406170	0.97[ASN][1000 genomes]
rs7406324	0.92[CHB][hapmap]
rs7406910	1.00[JPT][hapmap]
rs7503053	0.83[CHB][hapmap]
rs890431	1.00[JPT][hapmap]
rs9221	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs9903182	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9907987	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.97[ASN][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2740752	KAT2A	cis	cerebellum	SCAN
rs2740752	SPOP	cis	parietal	SCAN
rs2740752	C17orf88	cis	cerebellum	SCAN
rs2740752	SKAP1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46658800-46665800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr17:46661600-46667000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr17:46662000-46665200	Active TSS	Colon Smooth Muscle	Colon
4	chr17:46662400-46665000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr17:46662400-46665000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
6	chr17:46662400-46665600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr17:46662400-46668000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr17:46663200-46664800	Transcr. at gene 5' and 3'	NHLF	lung
9	chr17:46663200-46665400	Flanking Active TSS	Colonic Mucosa	Colon
10	chr17:46663200-46672000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr17:46663400-46666400	Enhancers	Lung	lung
12	chr17:46663600-46664800	Bivalent Enhancer	NH-A	brain
13	chr17:46663600-46665000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
14	chr17:46663600-46665800	Weak transcription	K562	blood
15	chr17:46663800-46665400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr17:46663800-46665400	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr17:46663800-46665600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr17:46663800-46665600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr17:46663800-46665600	Bivalent Enhancer	Liver	Liver
20	chr17:46663800-46665800	Enhancers	Spleen	Spleen
21	chr17:46663800-46666800	Enhancers	A549	lung
22	chr17:46663800-46669600	Weak transcription	Pancreas	Pancrea
23	chr17:46664000-46664800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr17:46664000-46665000	Bivalent Enhancer	Placenta	Placenta
25	chr17:46664000-46665200	Flanking Active TSS	Fetal Kidney	kidney
26	chr17:46664000-46665200	Weak transcription	HMEC	breast
27	chr17:46664000-46665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:46664000-46665600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr17:46664000-46666400	Enhancers	HSMM	muscle
30	chr17:46664000-46666600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:46664000-46667600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr17:46664000-46667800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
33	chr17:46664000-46668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:46664000-46670000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:46664200-46664800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
36	chr17:46664200-46665600	Flanking Bivalent TSS/Enh	Fetal Lung	lung
37	chr17:46664200-46666000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr17:46664200-46666800	Enhancers	HUVEC	blood vessel
39	chr17:46664400-46664800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
40	chr17:46664400-46664800	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr17:46664400-46665200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr17:46664400-46665400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr17:46664400-46665400	Enhancers	HSMMtube	muscle
44	chr17:46664400-46666000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:46664400-46666400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr17:46664400-46666800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr17:46664600-46664800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
48	chr17:46664600-46665000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr17:46664600-46665400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr17:46664600-46665600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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