Variant report

Variant	rs28506072
Chromosome Location	chr1:180466684-180466685
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	chr1:180446432..180448088-chr1:180465802..180468652,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10737342	0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10798752	0.89[ASN][1000 genomes]
rs10798753	0.89[ASN][1000 genomes]
rs10798754	0.89[ASN][1000 genomes]
rs10798761	0.89[ASN][1000 genomes]
rs10798767	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10913969	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913970	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10913994	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10914002	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10914007	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12024156	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034669	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039933	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12045123	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12045636	0.85[ASN][1000 genomes]
rs12085808	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12091722	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142124	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12402815	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12403665	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12404209	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12405902	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12407122	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12691484	0.89[ASN][1000 genomes]
rs1341924	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1418102	0.89[ASN][1000 genomes]
rs16856087	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1890731	0.93[ASN][1000 genomes]
rs1970400	0.80[ASN][1000 genomes]
rs2877399	0.89[ASN][1000 genomes]
rs2877415	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3737584	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806300	0.95[ASN][1000 genomes]
rs3806301	0.83[ASN][1000 genomes]
rs4424469	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4436345	0.89[ASN][1000 genomes]
rs4483365	0.89[ASN][1000 genomes]
rs4543756	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4562579	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4593778	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4642852	0.89[ASN][1000 genomes]
rs4652495	0.88[ASN][1000 genomes]
rs4652496	0.89[ASN][1000 genomes]
rs4652498	0.89[ASN][1000 genomes]
rs4652499	0.89[ASN][1000 genomes]
rs55874160	0.89[ASN][1000 genomes]
rs60286873	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425625	0.89[ASN][1000 genomes]
rs6425634	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425641	0.83[ASN][1000 genomes]
rs6657492	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6659513	0.89[ASN][1000 genomes]
rs6661208	0.89[ASN][1000 genomes]
rs6678216	0.89[ASN][1000 genomes]
rs6680368	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6687442	0.83[ASN][1000 genomes]
rs6687549	0.83[ASN][1000 genomes]
rs6699585	0.82[ASN][1000 genomes]
rs6704334	0.82[ASN][1000 genomes]
rs6704437	0.82[ASN][1000 genomes]
rs72720915	0.93[ASN][1000 genomes]
rs72720917	0.93[ASN][1000 genomes]
rs7526189	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7538219	0.89[ASN][1000 genomes]
rs7538303	0.89[ASN][1000 genomes]
rs7539910	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7544585	0.89[ASN][1000 genomes]
rs822706	0.86[ASN][1000 genomes]
rs9701037	0.94[ASN][1000 genomes]
rs9726041	0.83[ASN][1000 genomes]
rs9729819	0.85[ASN][1000 genomes]
rs9730180	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
2	chr1:180428000-180470000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:180431200-180470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:180432000-180470600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:180434200-180470200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:180435200-180469000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:180437600-180470400	Weak transcription	Right Ventricle	heart
8	chr1:180437600-180470600	Weak transcription	Spleen	Spleen
9	chr1:180437600-180471000	Weak transcription	Lung	lung
10	chr1:180440000-180469000	Weak transcription	HSMMtube	muscle
11	chr1:180440200-180468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:180440200-180469000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:180443400-180468200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:180444800-180470600	Weak transcription	Esophagus	oesophagus
15	chr1:180447000-180470400	Weak transcription	Colonic Mucosa	Colon
16	chr1:180447800-180469000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:180448400-180470200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:180449200-180469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:180449400-180466800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:180452000-180469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr1:180452000-180470000	Weak transcription	Fetal Heart	heart
22	chr1:180452200-180467000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:180453200-180467400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:180453800-180470600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:180454600-180470600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:180454800-180468600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:180455000-180468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:180455400-180470000	Weak transcription	Liver	Liver
29	chr1:180455600-180469000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:180455600-180469000	Weak transcription	Psoas Muscle	Psoas
31	chr1:180455600-180469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:180455600-180469400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:180455600-180469400	Weak transcription	Thymus	Thymus
34	chr1:180455600-180469600	Weak transcription	Gastric	stomach
35	chr1:180455600-180470200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:180455600-180470200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:180455600-180470200	Weak transcription	Brain Substantia Nigra	brain
38	chr1:180455600-180471000	Weak transcription	Left Ventricle	heart
39	chr1:180455800-180467200	Weak transcription	A549	lung
40	chr1:180455800-180468800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:180455800-180468800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:180455800-180468800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:180455800-180469000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:180456000-180470200	Weak transcription	Adipose Nuclei	Adipose
45	chr1:180456000-180471000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr1:180456400-180468200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:180456400-180470200	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:180456600-180470200	Weak transcription	Small Intestine	intestine
49	chr1:180456800-180468200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:180456800-180470000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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