Variant report

Variant	rs16861025
Chromosome Location	chr3:113184298-113184299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:113184124..113185846-chr3:113185911..113187476,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11919330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11920635	0.87[YRI][hapmap]
rs11920725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922598	0.91[JPT][hapmap]
rs11922838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11924109	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11926687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513288	0.91[JPT][hapmap];0.94[EUR][1000 genomes]
rs16845106	1.00[JPT][hapmap]
rs16845109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845110	0.85[YRI][hapmap]
rs16860962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860995	0.88[YRI][hapmap]
rs16861014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861059	0.88[YRI][hapmap]
rs16861077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861109	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes]
rs16861130	0.84[JPT][hapmap]
rs16861165	0.84[JPT][hapmap]
rs16861217	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs17255950	0.91[EUR][1000 genomes]
rs17256551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17256752	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17322613	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17325024	0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs1906141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989359	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes]
rs2129431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254267	0.84[JPT][hapmap]
rs2271496	0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs2291412	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306068	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2306070	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2399486	0.84[JPT][hapmap]
rs28472841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35758075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35812463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732799	0.84[JPT][hapmap]
rs3814399	1.00[JPT][hapmap]
rs4331647	0.84[JPT][hapmap]
rs4508746	0.84[JPT][hapmap]
rs4580515	0.84[JPT][hapmap]
rs56685963	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56772417	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57115529	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57164268	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57366942	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58905600	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58988763	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59271111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59493419	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59673391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59742486	0.84[EUR][1000 genomes]
rs60582065	0.84[EUR][1000 genomes]
rs60697865	0.91[EUR][1000 genomes]
rs60940543	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61065093	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61575357	0.87[EUR][1000 genomes]
rs61594119	0.84[EUR][1000 genomes]
rs6438150	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438151	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776729	0.84[JPT][hapmap]
rs6776974	0.84[JPT][hapmap]
rs6780755	0.84[JPT][hapmap]
rs6782784	0.84[JPT][hapmap]
rs6783691	1.00[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6790846	0.84[JPT][hapmap]
rs6805231	0.84[JPT][hapmap]
rs735	0.91[EUR][1000 genomes]
rs7610552	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7620700	0.84[JPT][hapmap]
rs7646262	0.84[JPT][hapmap]
rs9832953	0.82[JPT][hapmap]
rs9848190	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113074400-113184400	Weak transcription	Hela-S3	cervix
2	chr3:113146000-113191000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:113160200-113190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:113160400-113186800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:113160400-113188800	Weak transcription	Colonic Mucosa	Colon
6	chr3:113160400-113191200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:113160400-113192800	Weak transcription	Stomach Mucosa	stomach
8	chr3:113160600-113188600	Weak transcription	Psoas Muscle	Psoas
9	chr3:113160600-113190600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:113160600-113203800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:113160800-113187000	Weak transcription	HUVEC	blood vessel
12	chr3:113160800-113187600	Weak transcription	NHLF	lung
13	chr3:113160800-113189400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:113160800-113189400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:113160800-113189600	Weak transcription	NHEK	skin
16	chr3:113160800-113203800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:113160800-113203800	Weak transcription	Aorta	Aorta
18	chr3:113160800-113224800	Weak transcription	Placenta	Placenta
19	chr3:113160800-113232600	Weak transcription	Right Ventricle	heart
20	chr3:113161000-113189600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:113161000-113189600	Weak transcription	Brain Substantia Nigra	brain
22	chr3:113161000-113190800	Weak transcription	K562	blood
23	chr3:113161400-113192200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:113164000-113185600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:113166200-113188800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:113166600-113186400	Weak transcription	A549	lung
27	chr3:113166600-113203800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:113169000-113186600	Weak transcription	Small Intestine	intestine
29	chr3:113169800-113191600	Weak transcription	Fetal Brain Male	brain
30	chr3:113172600-113187000	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:113172600-113203800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:113172800-113232800	Weak transcription	HSMMtube	muscle
33	chr3:113173200-113187000	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:113173800-113190200	Weak transcription	Fetal Heart	heart
35	chr3:113174600-113190200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:113175000-113190600	Weak transcription	Brain Germinal Matrix	brain
37	chr3:113176200-113186600	Weak transcription	Osteobl	bone
38	chr3:113176400-113233200	Weak transcription	Gastric	stomach
39	chr3:113177000-113186200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:113177400-113225800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:113177600-113224400	Weak transcription	Spleen	Spleen
42	chr3:113177800-113187000	Weak transcription	Lung	lung
43	chr3:113178000-113184800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:113178600-113184400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:113179400-113186400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:113179400-113186800	Weak transcription	GM12878-XiMat	blood
47	chr3:113179400-113187400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:113179600-113186200	Weak transcription	HepG2	liver
49	chr3:113179600-113186400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr3:113179600-113186400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links