Variant report

Variant	rs4788576
Chromosome Location	chr16:71934105-71934106
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:71934002-71934260	K562	blood:	n/a	n/a
2	POLR2A	chr16:71933827-71934133	GM12878	blood:	n/a	n/a
3	ZNF384	chr16:71933953-71934646	GM12878	blood:	n/a	n/a
4	POLR2A	chr16:71934075-71934459	HepG2	liver:	n/a	n/a
5	ZNF384	chr16:71933934-71934549	K562	blood:	n/a	n/a
6	POLR2A	chr16:71934104-71934903	GM12878	blood:	n/a	n/a
7	POLR2A	chr16:71934068-71934730	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71931575..71934137-chr16:71950822..71953492,2	MCF-7	breast:
2	chr16:71931560..71934913-chr16:71937416..71939939,3	K562	blood:
3	chr16:71933089..71936060-chr16:71938711..71940740,2	MCF-7	breast:
4	chr16:71932998..71934672-chr16:71946050..71948887,2	K562	blood:
5	chr16:71933462..71935893-chr16:71936421..71939134,2	MCF-7	breast:
6	chr16:71926844..71931687-chr16:71933054..71938868,11	MCF-7	breast:
7	chr16:71933405..71937193-chr16:71939159..71943581,7	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF821	TF binding region
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11075908	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11075911	0.90[EUR][1000 genomes]
rs11648353	0.89[EUR][1000 genomes]
rs11648530	0.90[EUR][1000 genomes]
rs11649672	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11859903	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12102548	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12444829	0.97[EUR][1000 genomes]
rs12447045	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12449139	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12599192	0.92[EUR][1000 genomes]
rs12921084	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12926041	0.93[EUR][1000 genomes]
rs12926300	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12930744	0.90[EUR][1000 genomes]
rs12935795	0.89[EUR][1000 genomes]
rs13329779	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1834034	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1834035	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1981874	0.91[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008675	0.87[EUR][1000 genomes]
rs2018384	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288029	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288031	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335709	0.97[EUR][1000 genomes]
rs2335710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335711	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2335713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335714	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2335715	0.91[EUR][1000 genomes]
rs28697038	0.95[EUR][1000 genomes]
rs2878492	0.90[EUR][1000 genomes]
rs3794692	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4788446	0.80[EUR][1000 genomes]
rs4788447	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4788449	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788562	0.88[EUR][1000 genomes]
rs4788563	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4788564	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788566	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788570	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788571	0.95[EUR][1000 genomes]
rs4788573	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4788581	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4788582	0.91[EUR][1000 genomes]
rs4788584	0.90[EUR][1000 genomes]
rs4788585	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs62053803	0.90[EUR][1000 genomes]
rs6499533	1.00[JPT][hapmap]
rs6499542	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[EUR][1000 genomes]
rs6499545	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6499551	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6499552	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6558	1.00[JPT][hapmap]
rs7184437	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7184486	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs7187129	0.89[EUR][1000 genomes]
rs7193731	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7194858	1.00[JPT][hapmap]
rs7204708	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs7205154	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8044342	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8046859	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8050488	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8050651	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs8051038	0.92[EUR][1000 genomes]
rs8054111	0.87[EUR][1000 genomes]
rs8054175	0.87[EUR][1000 genomes]
rs8054403	0.86[EUR][1000 genomes]
rs8057124	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8058118	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8059053	0.97[EUR][1000 genomes]
rs8062946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8063324	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs8063403	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9302631	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9302632	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9806882	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9806905	0.88[EUR][1000 genomes]
rs9888748	0.89[EUR][1000 genomes]
rs9889011	0.89[EUR][1000 genomes]
rs9921412	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs9932922	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9934803	0.92[EUR][1000 genomes]
rs9934812	0.92[EUR][1000 genomes]
rs9937936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];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	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4788576	PSMD7	cis	parietal	SCAN
rs4788576	SNTB2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71930400-71934800	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr16:71930600-71934200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:71930800-71934400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr16:71930800-71934800	Enhancers	Small Intestine	intestine
5	chr16:71930800-71935400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr16:71930800-71935400	Enhancers	Primary T cells fromperipheralblood	blood
7	chr16:71930800-71943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:71930800-71944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr16:71931000-71934600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:71931000-71934600	Enhancers	Colon Smooth Muscle	Colon
13	chr16:71931000-71937000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr16:71931000-71937800	Enhancers	Primary B cells from peripheral blood	blood
15	chr16:71931000-71942800	Weak transcription	Fetal Heart	heart
16	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr16:71931000-71949600	Weak transcription	NHEK	skin
18	chr16:71931200-71934200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr16:71931200-71934200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr16:71931200-71934400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:71931200-71934600	Enhancers	Brain Hippocampus Middle	brain
22	chr16:71931200-71934800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:71931200-71935000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:71931200-71935600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr16:71931200-71935800	Weak transcription	NH-A	brain
26	chr16:71931200-71936600	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr16:71931200-71936800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr16:71931200-71936800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr16:71931200-71936800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr16:71931200-71937000	Weak transcription	Brain Germinal Matrix	brain
31	chr16:71931200-71938200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr16:71931200-71940600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr16:71931200-71942800	Weak transcription	HSMM	muscle
34	chr16:71931200-71943000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr16:71931200-71943000	Weak transcription	Fetal Lung	lung
36	chr16:71931200-71943000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr16:71931200-71943200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr16:71931200-71944800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr16:71931200-71946600	Weak transcription	A549	lung
40	chr16:71931200-71949800	Weak transcription	Esophagus	oesophagus
41	chr16:71931200-71950000	Weak transcription	HMEC	breast
42	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr16:71931400-71934400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:71931400-71942600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr16:71931400-71949400	Weak transcription	Fetal Kidney	kidney
46	chr16:71931600-71934200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr16:71931600-71934200	Weak transcription	Fetal Brain Female	brain
48	chr16:71931600-71934200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr16:71931600-71934800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr16:71931600-71937200	Weak transcription	Fetal Intestine Large	intestine

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