Variant report

Variant	rs16855099
Chromosome Location	chr1:179978893-179978894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179973630..179975308-chr1:179977263..179979537,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10442618	0.92[ASN][1000 genomes]
rs10494524	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12118985	0.92[ASN][1000 genomes]
rs12120418	0.92[ASN][1000 genomes]
rs12121834	0.92[ASN][1000 genomes]
rs12121845	0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12123139	0.92[ASN][1000 genomes]
rs12123201	0.84[ASN][1000 genomes]
rs12123560	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12124265	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12125556	0.92[ASN][1000 genomes]
rs12125693	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12125893	0.92[ASN][1000 genomes]
rs12130479	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12130675	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12132694	0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs12134536	0.92[ASN][1000 genomes]
rs12135751	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12135828	0.92[ASN][1000 genomes]
rs12138201	0.92[ASN][1000 genomes]
rs12138974	0.92[ASN][1000 genomes]
rs12139323	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12139412	1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs12139761	0.92[ASN][1000 genomes]
rs12140235	0.92[ASN][1000 genomes]
rs12140589	0.84[AFR][1000 genomes]
rs12140868	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12141817	1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs12144275	0.84[ASN][1000 genomes]
rs12145411	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12184270	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16843139	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs16854997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16855014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16855019	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855021	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855022	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855025	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855048	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16855049	1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs16855052	0.84[ASN][1000 genomes]
rs16855070	0.84[AFR][1000 genomes]
rs16855103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855107	0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16855110	0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855130	0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs16855144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855259	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855268	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855270	0.92[ASN][1000 genomes]
rs16855286	1.00[CHB][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3856048	0.84[ASN][1000 genomes]
rs41267622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4266842	0.92[ASN][1000 genomes]
rs4278337	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4460595	1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs4652469	0.89[CHD][hapmap]
rs57165548	0.84[ASN][1000 genomes]
rs58316647	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58463801	0.84[ASN][1000 genomes]
rs58749862	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58844263	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59132689	0.92[ASN][1000 genomes]
rs60064848	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60895715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60927554	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60972670	0.92[ASN][1000 genomes]
rs60976015	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61014689	0.84[ASN][1000 genomes]
rs61242295	0.92[ASN][1000 genomes]
rs73032352	0.84[ASN][1000 genomes]
rs73032390	0.92[ASN][1000 genomes]
rs73032397	0.92[ASN][1000 genomes]
rs73034408	0.92[ASN][1000 genomes]
rs73034486	0.92[ASN][1000 genomes]
rs73039990	0.84[ASN][1000 genomes]
rs73039999	0.84[ASN][1000 genomes]
rs73040001	0.84[ASN][1000 genomes]
rs7525395	1.00[JPT][hapmap]
rs9699897	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179938000-179983200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:179938600-179983200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:179938600-179984600	Weak transcription	Lung	lung
4	chr1:179939000-179989000	Weak transcription	Gastric	stomach
5	chr1:179941400-180031800	Weak transcription	Spleen	Spleen
6	chr1:179946400-179983000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:179946400-179989200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:179946600-179983200	Weak transcription	Brain Angular Gyrus	brain
9	chr1:179947800-179989400	Weak transcription	Small Intestine	intestine
10	chr1:179948600-179983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:179949400-179980600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:179950000-179980600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:179955000-179989200	Weak transcription	Aorta	Aorta
14	chr1:179955800-179983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:179956800-179989400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:179958600-179991600	Weak transcription	Fetal Brain Male	brain
17	chr1:179959200-179983200	Weak transcription	NHLF	lung
18	chr1:179959600-179983000	Weak transcription	Colonic Mucosa	Colon
19	chr1:179962000-179989200	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:179962400-179983200	Weak transcription	A549	lung
21	chr1:179964000-179989200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:179964000-180014200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:179964400-179984600	Weak transcription	HUVEC	blood vessel
24	chr1:179964600-179984200	Weak transcription	Fetal Intestine Small	intestine
25	chr1:179965800-180013200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:179966400-179981000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:179966400-179981600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:179966400-179983200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:179966400-179983200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:179966600-179979800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:179966600-179981000	Weak transcription	HSMM	muscle
32	chr1:179966600-179983000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:179966600-179983000	Weak transcription	Fetal Brain Female	brain
34	chr1:179966600-179983000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:179966600-179983000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:179966600-179983200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:179966600-179983200	Weak transcription	Left Ventricle	heart
38	chr1:179966600-179988000	Weak transcription	Pancreas	Pancrea
39	chr1:179966600-179988000	Weak transcription	Right Ventricle	heart
40	chr1:179966800-179983200	Weak transcription	Esophagus	oesophagus
41	chr1:179966800-179983200	Weak transcription	Fetal Stomach	stomach
42	chr1:179967000-179983200	Weak transcription	HepG2	liver
43	chr1:179968000-179983000	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:179969800-179983000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:179971600-179997400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:179971800-179979000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:179972000-179982800	Weak transcription	Osteobl	bone
49	chr1:179972000-179983400	Weak transcription	HMEC	breast
50	chr1:179972200-179983200	Weak transcription	NHEK	skin

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