Variant report

Variant	rs9289712
Chromosome Location	chr3:145785706-145785707
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	chr3:145783644..145786560-chr3:145833867..145835451,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs12171294	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496198	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12496358	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695808	0.90[ASN][1000 genomes]
rs13063887	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13088158	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1349214	0.89[ASN][1000 genomes]
rs1349215	0.90[ASN][1000 genomes]
rs1375578	0.81[EUR][1000 genomes]
rs1375581	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1375582	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375584	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375587	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449438	0.81[EUR][1000 genomes]
rs1449439	0.81[EUR][1000 genomes]
rs1449440	0.92[ASN][1000 genomes]
rs1449441	0.99[ASN][1000 genomes]
rs1449444	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449445	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449450	0.88[ASN][1000 genomes]
rs1449451	0.86[ASN][1000 genomes]
rs1512900	0.86[ASN][1000 genomes]
rs1512901	0.86[ASN][1000 genomes]
rs1530741	0.85[ASN][1000 genomes]
rs1562699	0.87[ASN][1000 genomes]
rs1584489	0.81[EUR][1000 genomes]
rs1613698	0.88[ASN][1000 genomes]
rs1613796	0.88[ASN][1000 genomes]
rs1707465	0.86[ASN][1000 genomes]
rs1707466	0.86[ASN][1000 genomes]
rs1707471	0.85[ASN][1000 genomes]
rs1707472	0.85[ASN][1000 genomes]
rs1707473	0.85[ASN][1000 genomes]
rs1707479	0.86[ASN][1000 genomes]
rs1900926	0.86[ASN][1000 genomes]
rs2029137	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2029138	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197908	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305274	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669396	0.85[ASN][1000 genomes]
rs2864792	0.90[ASN][1000 genomes]
rs2864793	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35399421	0.82[EUR][1000 genomes]
rs3762691	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792339	0.87[ASN][1000 genomes]
rs3792341	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804660	0.90[ASN][1000 genomes]
rs3804661	0.90[ASN][1000 genomes]
rs3804664	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804665	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3804666	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3804668	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3804669	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3804670	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3816399	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3828381	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681111	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681112	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681113	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681294	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681299	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440415	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6440417	0.91[ASN][1000 genomes]
rs6440419	0.90[ASN][1000 genomes]
rs6710	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770862	0.81[EUR][1000 genomes]
rs6783601	0.88[ASN][1000 genomes]
rs6799720	0.88[ASN][1000 genomes]
rs6800294	0.88[ASN][1000 genomes]
rs6800434	0.88[ASN][1000 genomes]
rs6801418	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6802384	0.88[ASN][1000 genomes]
rs7431590	0.99[ASN][1000 genomes]
rs7614409	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7617913	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639592	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641322	0.86[EUR][1000 genomes]
rs764755	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs895929	0.88[ASN][1000 genomes]
rs895930	0.88[ASN][1000 genomes]
rs9289713	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289714	0.92[ASN][1000 genomes]
rs9289715	0.92[ASN][1000 genomes]
rs9289716	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289717	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289718	0.86[ASN][1000 genomes]
rs959329	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs963591	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809099	0.88[ASN][1000 genomes]
rs9813047	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822426	0.88[ASN][1000 genomes]
rs9828112	0.92[ASN][1000 genomes]
rs9836521	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9842036	0.88[ASN][1000 genomes]
rs9842560	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9849076	0.81[EUR][1000 genomes]
rs9852153	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9852725	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858081	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9858095	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9862005	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9862237	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9865802	0.92[ASN][1000 genomes]
rs9867807	0.81[EUR][1000 genomes]
rs9874388	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874627	0.82[EUR][1000 genomes]
rs9877411	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9878166	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9881251	0.92[ASN][1000 genomes]
rs9882583	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145768800-145788400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:145774600-145787200	Weak transcription	Esophagus	oesophagus
3	chr3:145774600-145795400	Weak transcription	Aorta	Aorta
4	chr3:145775400-145786600	Weak transcription	HepG2	liver
5	chr3:145776200-145786000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:145776200-145786400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:145776600-145787200	Weak transcription	HMEC	breast
8	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
10	chr3:145778600-145789000	Weak transcription	Left Ventricle	heart
11	chr3:145778800-145788400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:145779000-145789600	Weak transcription	Fetal Heart	heart
13	chr3:145779400-145788800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
15	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
17	chr3:145780800-145786600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr3:145780800-145793800	Weak transcription	Ovary	ovary
19	chr3:145780800-145793800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:145781000-145788400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:145781000-145788800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
24	chr3:145782600-145786200	Weak transcription	Liver	Liver
25	chr3:145782600-145786400	Weak transcription	Fetal Intestine Large	intestine
26	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
27	chr3:145783600-145785800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:145783600-145785800	Genic enhancers	Osteobl	bone
29	chr3:145783800-145786400	Weak transcription	Fetal Lung	lung
30	chr3:145784000-145789400	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:145784400-145788400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:145784600-145790400	Weak transcription	NHLF	lung
34	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:145784800-145789600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:145784800-145794000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:145785000-145788000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:145785000-145789600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:145785200-145786000	Weak transcription	NH-A	brain
40	chr3:145785200-145788400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:145785200-145806400	Weak transcription	Colonic Mucosa	Colon
42	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:145785400-145785800	Weak transcription	HSMMtube	muscle
44	chr3:145785400-145786000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:145785400-145786000	Weak transcription	HUVEC	blood vessel
46	chr3:145785400-145786200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:145785400-145786400	Enhancers	A549	lung
48	chr3:145785400-145787000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:145785400-145788600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:145785400-145789400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links