Variant report

Variant	rs6499552
Chromosome Location	chr16:71943169-71943170
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71936147..71938955-chr16:71940995..71943560,3	K562	blood:
2	chr16:71935084..71939148-chr16:71940742..71943811,5	MCF-7	breast:
3	chr16:71942932..71945142-chr16:71984421..71987167,2	K562	blood:
4	chr16:71933405..71937193-chr16:71939159..71943581,7	MCF-7	breast:
5	chr16:71941557..71944362-chr16:71947256..71950038,2	K562	blood:

Variant related genes	Relation type
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11075908	1.00[EUR][1000 genomes]
rs11075911	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648353	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11648530	0.91[EUR][1000 genomes]
rs11649672	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12102548	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12444829	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12447045	0.95[EUR][1000 genomes]
rs12449139	0.99[EUR][1000 genomes]
rs12599192	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12921084	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12926041	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12926300	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12930744	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12935795	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13329779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1834034	0.91[EUR][1000 genomes]
rs1834035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1981874	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2008675	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2018384	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2288029	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2288031	0.96[EUR][1000 genomes]
rs2335709	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2335710	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2335711	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2335712	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2335713	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2335714	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2335715	0.92[EUR][1000 genomes]
rs28697038	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2878492	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4788446	0.81[EUR][1000 genomes]
rs4788447	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4788449	1.00[EUR][1000 genomes]
rs4788562	0.88[EUR][1000 genomes]
rs4788563	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4788564	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788566	0.93[EUR][1000 genomes]
rs4788570	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4788571	0.96[EUR][1000 genomes]
rs4788573	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4788576	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4788582	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4788584	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4788585	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62053803	0.91[EUR][1000 genomes]
rs6499542	0.83[EUR][1000 genomes]
rs6499545	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6499551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184437	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7184486	0.90[EUR][1000 genomes]
rs7187129	0.90[EUR][1000 genomes]
rs7193731	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7204708	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7205154	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs8044342	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs8046859	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8050488	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8050651	0.94[EUR][1000 genomes]
rs8051038	0.93[EUR][1000 genomes]
rs8054111	0.88[EUR][1000 genomes]
rs8054175	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8054403	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8057124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8058118	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8059053	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8062946	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8063324	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8063403	1.00[EUR][1000 genomes]
rs9302631	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302632	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806882	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9806905	0.89[EUR][1000 genomes]
rs9888748	0.90[EUR][1000 genomes]
rs9889011	0.90[EUR][1000 genomes]
rs9921412	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932922	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9934803	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9934812	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9937936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71930800-71943200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr16:71930800-71944200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr16:71930800-71950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:71930800-71951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr16:71931000-71949400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr16:71931000-71949600	Weak transcription	NHEK	skin
7	chr16:71931200-71943200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr16:71931200-71944800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr16:71931200-71946600	Weak transcription	A549	lung
10	chr16:71931200-71949800	Weak transcription	Esophagus	oesophagus
11	chr16:71931200-71950000	Weak transcription	HMEC	breast
12	chr16:71931200-71956200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr16:71931400-71949400	Weak transcription	Fetal Kidney	kidney
14	chr16:71931600-71944400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr16:71932000-71943200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr16:71932600-71951800	Weak transcription	Colonic Mucosa	Colon
17	chr16:71933400-71948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr16:71933400-71949000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:71933400-71950200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr16:71934200-71949600	Weak transcription	Placenta	Placenta
21	chr16:71934400-71945600	Weak transcription	Aorta	Aorta
22	chr16:71934400-71951000	Weak transcription	Fetal Brain Male	brain
23	chr16:71934600-71943200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr16:71934600-71943200	Weak transcription	NHDF-Ad	bronchial
25	chr16:71934600-71943400	Weak transcription	Colon Smooth Muscle	Colon
26	chr16:71934600-71946600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr16:71934600-71948400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:71934600-71948800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr16:71934600-71949000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr16:71934600-71949600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:71934800-71943200	Weak transcription	Stomach Mucosa	stomach
32	chr16:71934800-71946600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr16:71934800-71948200	Weak transcription	HUVEC	blood vessel
34	chr16:71935000-71946600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:71935200-71950200	Weak transcription	NHLF	lung
36	chr16:71936000-71943400	Weak transcription	Adipose Nuclei	Adipose
37	chr16:71936000-71943600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr16:71936000-71948200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr16:71936000-71948600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:71936200-71943200	Weak transcription	NH-A	brain
41	chr16:71936200-71946600	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr16:71937000-71943200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr16:71937200-71952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:71937600-71947400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr16:71938000-71945000	Weak transcription	K562	blood
46	chr16:71938000-71949800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr16:71938200-71943800	Weak transcription	Liver	Liver
48	chr16:71938200-71945600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr16:71938600-71943200	Weak transcription	Ovary	ovary
50	chr16:71938600-71943200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links